cbielow / ptxqc Goto Github PK

If low MS/MS identification rates are observed without clear indications of origin (e.g. intensities are high, samples are mass-calibrated, etc) it might be beneficial to re-run MaxQuant allowing more variable modifications, e.g.

• carbamylation (N-Term, lysine), due to improper denaturing conditions using urea (temp, freshness)
• deamidation (asp, glu), due to prolonged digestion at mildly basic pH

To see the impact of these mods (beside the overall number of identified peptides/proteins after FDR), a Pareto chart (barchart) of modifications will be useful.

Hi Chris,

I freshly installed PTQXC v 0.92.3 from Github, following your instructions. Everything went fine during installation, using R-3.4.3 and Windows 10.

When I tried to produce a report by drag-and-drop, I ran into an error. Checking the log file, I saw that PTQXC expected an mqpar.xml in the txt folder, so I copied the file to that location. However, the error persists.

There seem to be two problems:

1. Many columns in the .txt-files are not recognized as numeric.
2. The command line ended in (I manually added this to the log file for convience):

Quitting from lines 75-111 (PTXQC_report_template.Rmd)

Error in FUN(X[[i]], ...) : Objekt 'PC2' nicht gefunden
Zusätzlich: Warnmeldungen:
1: Using alpha for a disecrete variable is not advised.
2: Using alpha for a disecrete variable is not advised.

No PDF or HTML file was created. Only one PNG file was created in the folder figure-html. I attached all files created by PTXQC here.

Greetings,
Florian

new metric: compute the overlap of genuine peptide IDs between neighbouring fractions (since this is used by MaxQuant for alignment). If the overlap is sparse, the alignment cannot be reliably calculated (which should also be apparent in the MBR metrics). In this case it might be better to use distant fractions for the affected files in order to to avoid potential false positives by MaxQuant"s MBR

with incomplete txt folders, the following message can show up during report creation:

Starting to work on Average Overall Quality ...
Error in workerFcn(.self, ...) : 
  AverageQual_qc::workerFcn(): input empty!

cause: if no metric could be computed, e.g. because only parameters.txt was provided, the heatmap generation fails.

e.g. using R^2 could hint at non-specific sample loss in some samples, i.e. overall reduced reproducibility and false positive biomarkers, due to different sample handling and materials (tubes, addition of compounds, adsorption, ...). This works well only for technical replicates, since different biol. conditions might obviously not be perfectly correlated.
Reference could be the sample whose median intensity is representative (rather than using the median of each peptide, since this destroys the connection between peptides)

Hi Chris,
I have PTXQC installed in C:\PTXQC. I tried to install the latest fix by running the R-scripts:

if (!require(devtools, quietly = TRUE)) install.packages("devtools")
library("devtools")
install_github("cbielow/PTXQC", build_vignettes = TRUE)

This gave the following messages:

Installing PTXQC
Installing 1 package: digest
Installing package into ‘C:/Users/LCMS/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.3/digest_0.6.10.zip'
Content type 'application/zip' length 169641 bytes (165 KB)
downloaded 165 KB

package ‘digest’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘digest’

The downloaded binary packages are in
C:\Users\LCMS\AppData\Local\Temp\Rtmpk3Ie2C\downloaded_packages
"C:/PROGRA1/R/R-331.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD build
"C:\Users\LCMS\AppData\Local\Temp\Rtmpk3Ie2C\devtools1a243e78436c\cbielow-PTXQC-e37facc" --no-resave-data --no-manual

• checking for file 'C:\Users\LCMS\AppData\Local\Temp\Rtmpk3Ie2C\devtools1a243e78436c\cbielow-PTXQC-e37facc/DESCRIPTION' ... OK
• preparing 'PTXQC':
• checking DESCRIPTION meta-information ... OK

• installing the package to build vignettes
  Warning: running command '"C:/PROGRA1/R/R-331.0/bin/x64/Rcmd.exe" INSTALL -l "C:\Users\LCMS\AppData\Local\Temp\Rtmp0e3KiO\Rinst322851fc84a" --no-multiarch "C:/Users/LCMS/AppData/Local/Temp/Rtmp0e3KiO/Rbuild3228b67691b/PTXQC"' had status 1

• installing source package 'PTXQC' ...
  ** R
  ** inst
  ** preparing package for lazy loading
  Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  there is no package called 'digest'
  ERROR: lazy loading failed for package 'PTXQC'

• removing 'C:/Users/LCMS/AppData/Local/Temp/Rtmp0e3KiO/Rinst322851fc84a/PTXQC'

  ERROR: package installation failed
  Error: Command failed (1)

Now trying to run PTXQC on a MaxQuant result it used to work on before gives the following messages in a Windows command screen:

This batch file allows invoking 'createQC_dragNdrop.bat'
with a YAML config file which resides in this directory.

Using 'C:\PTXQC\dragNdrop\QC-dragdrop\config.yaml' as YAML config

This batch file is used to invoke the QC script by drag'n'dropping of
a MaxQuant txt folder (or any file within) onto this .bat file.
Within the same txt folder, a QC report in Html/PDF format will be created.

First time installation of this script [for admins only]:
The script expects a certain structure to be present.
This .bat file expects a subfolder named '_internal'
which holds:
'R-3.3.0' Holds a complete R installation
(including all packages required to run the
PTXQC package)
'compute_QC_report.R' The R script that is invoked by this .bat

Found QC directory at 'C:\PTXQC\dragNdrop\QC-dragdrop_internal'

-- 'F:\2016\16_07_25_Moheb_Jos_Francesca\Francesca\combined\txt' is a directory
Txt folder is at 'F:\2016\16_07_25_Moheb_Jos_Francesca\Francesca\combined\txt'

Yaml file is: C:\PTXQC\dragNdrop\QC-dragdrop\config.yaml

Using YAML configuration file "C:\PTXQC\dragNdrop\QC-dragdrop\config.yaml"

Found R at '"C:\PTXQC\dragNdrop\QC-dragdrop_internal"\R-3.3.0\bin\x64\rscript.exe'.

Using YAML "C:\PTXQC\dragNdrop\QC-dragdrop\config.yaml" file and calling R now ...

Calling '"C:\PTXQC\dragNdrop\QC-dragdrop_internal"\R-3.3.0\bin\x64\rscript.exe --vanilla "C:\PTXQC\dragNdrop\QC-dragdrop_internal"\compute_QC_report.R F:\2016\16_07_25_Moheb_Jos_Francesca\Francesca\combined\txt "C:\PTXQC\dragNdrop\QC-dragdrop\config.yaml"'
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called 'digest'
Error: package or namespace load failed for 'PTXQC'
Execution halted
Failed folder F:\2016\16_07_25_Moheb_Jos_Francesca\Francesca\combined\txt. Does it exist and is writeable!?
Access is denied.

The error should be indicated above.
Common errors are (yours might be different)

• your R installation runs out of memory; especially if its 32bit
• the file 'C:\PTXQC\dragNdrop\QC-dragdrop_internal\compute_QC_report.R' is missing

If the error persists, follow the
instructions on https://github.com/cbielow/PTXQC
in the section 'Bug reporting'.

Leave this window open until the bug report is submitted

You can copy the text from this window by

1. right-clicking here
2. choose 'Select all'
3. press the 'Enter' key
4. paste it somewhere (issue ticket, email)
   This ensures that all text is available to debug the problem.
   Thanks!
   Press any key to continue . . .

Please tell me how to get PTXQC working again with the fix.
Thank you,
Sjef Boeren

In OpenMS the ITRAQAnalyzer will report the labeling efficiency for iTRAQ channels, i.e. how many spectra contain a certain reporter ion.
High values indicate successful chemical labeling, high amount of sample and few contamiants (usually not labeled since introduced post labeling).

Low values indicate that either of the above is not optimal, or that a large portion of proteins is not expressed in certain samples, but in others, e.g. if you mix yeast (labeled, 114, 115) + HEK (label 116, 117), then HEK peptides will lack the 114,115 label, whereas yeast peptides lack the 116,117 label.
Since HEK has more proteins/peptides, labeling efficiency in 114,115 will be lower, since we average over all MS/MS spectra.

The MQ APK files will probably suffice as the data source, but it might be time-consuming to parse them. Maybe we need to write a C(++) parser, since R is really not meant for this....

This also works for TMT of course.

Hi, me again, when install the PTXQC in my desktop, I have a probelm, which induced command failed. The error said: " It seems you should call rmarkdown::render() instead of knitr::knit2html() because PTXQC-Basic_Guide_for_R_users.Rmd appears to be an R Markdown v2 document."
my R version is R-3.2,3 (64 bit). Please help me! Thanks!

the installation command as follows:

if (!require(devtools, quietly = TRUE)) install.packages("devtools")
library("devtools")
source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
biocLite("Biobase")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) ‘Biobase’
试开URL’https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/Biobase_2.30.0.zip'
Content type 'application/zip' length 4227858 bytes (4.0 MB)
downloaded 4.0 MB

package ‘Biobase’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Administrator\AppData\Local\Temp\RtmpkvLked\downloaded_packages
Old packages: 'nlme'
Update all/some/none? [a/s/n]: a

有二进制版本的，但源代码版本是后来的:
binary source needs_compilation
nlme 3.1-123 3.1-124 TRUE

Binaries will be installed
试开URL’https://cran.rstudio.com/bin/windows/contrib/3.2/nlme_3.1-123.zip'
Content type 'application/zip' length 2149286 bytes (2.0 MB)
downloaded 2.0 MB

package ‘nlme’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Administrator\AppData\Local\Temp\RtmpkvLked\downloaded_packages

install_github("cbielow/PTXQC", build_vignettes = TRUE)
Downloading GitHub repo cbielow/PTXQC@master
Installing PTXQC
"D:/R/R-3.2.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD build
"C:\Users\Administrator\AppData\Local\Temp\RtmpkvLked\devtools74441935eae\cbielow-PTXQC-6322c99" --no-resave-data --no-manual

• checking for file 'C:\Users\Administrator\AppData\Local\Temp\RtmpkvLked\devtools74441935eae\cbielow-PTXQC-6322c99/DESCRIPTION' ... OK
• preparing 'PTXQC':
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ...Warning: 运行命令'"D:/R/R-32~1.3/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"'的状态是1
  ERROR
  Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc is not available. Please install both.
  错误: 处理标头'PTXQC-Basic_Guide_for_R_users.Rmd'失败，诊断信息为:
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because PTXQC-Basic_Guide_for_R_users.Rmd appears to be an R Markdown v2 document.
  停止执行
  错误: Command failed (1)

using a (customizable) rule set, e.g.

fail_ProteinCount = 0.6
if (score_proteinCount < fail_ProteinCount ) ## below 60% of target value
{
  flagAsFailed(raw_files[score_proteinCount < fail_ProteinCount ]);
}

currently unclear:

• best implementation practice (ruleset in YAML?)
• a default rule set (which metrics are important?)

Hi, Thanks for so great package for us
we have used PTXQC for long time, and it helps us a lot.
But recently, it does not work.
detail is that:
when go to the command:
r = createReport(txt_folder)
it reports a error:
Error in createReport(txt_folder) :
Argument txt_folder with value 'E:ping/shenghuahao/zhangchao/combined/txt' is not a valid directory

Maybe it because of upgrade of package,
So I re-install the package, but there comes another error:

"package ‘yaml’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘yaml’
"E:/software/R-3.2.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD build
"C:\Users\waters\AppData\Local\Temp\Rtmpcb0kmH\devtools77201644292\cbielow-PTXQC-4e736c6" --no-resave-data --no-manual

• checking for file 'C:\Users\waters\AppData\Local\Temp\Rtmpcb0kmH\devtools77201644292\cbielow-PTXQC-4e736c6/DESCRIPTION' ... OK
• preparing 'PTXQC':
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
  Warning: running command '"E:/software/R-32~1.3/bin/x64/Rcmd.exe" INSTALL -l "C:\Users\waters\AppData\Local\Temp\Rtmp40dupV\Rinst998c4cce6cf2" --no-multiarch "C:/Users/waters/AppData/Local/Temp/Rtmp40dupV/Rbuild998c47314e53/PTXQC"' had status 1
  -----------------------------------
  ERROR: dependencies 'plyr', 'reshape2', 'seqinr', 'yaml' are not available for package 'PTXQC'
• removing 'C:/Users/waters/AppData/Local/Temp/Rtmp40dupV/Rinst998c4cce6cf2/PTXQC'
  -----------------------------------
  ERROR: package installation failed
  Error: Command failed (1)"

Thanks!

Starting to work on MS^2*Scans: Intensity ... 
Warning: Ignoring unknown aesthetics: width 
Error in qualLinThresh(x$ratio - score_min_factor, t = score_max_factor -  : 
  qualLinThresh(): negative input 'x' not allowed! 

when MSMSScans.txt data shows very low total intensity compared to base peak.

Hi. Firstly, PTXQC is a very nice and useful tool. Thanks. When I installed and ran PTXQC and Pandoc the first time, everything went perfectly, and all the required reports were generated. However, since then, every time I try to run it, everything works EXCEPT the writing of the html report. Any ideas what is happening? I run it from R (simply using createReport(txt_folder)). Does Pandoc have to be in the windows PATH? Do I have to tell PTXQC where to look for Pandoc? When I installed Pandoc initially, it was installed in my /User/AppData folder (rather than Program Files). At present it is in my RStudio/bin directory. Could this be causing problems? Where should Pandoc be in my path? Thanks. Dean

Hi, Thanks for helping me!
I used maxquant （version: 1.5.1.0）LFQ （label free quant）to quant 40 single phase proteome profiling project. when I use PTXQC in R (i386 3.2.0), it report warning and error like follows, please help me! Thanks a lot!

"> txt_folder = "D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt"

r = createReport(txt_folder)
Reading file D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt/parameters.txt ...
Read 59 entries from D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt/parameters.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Reading file D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt/summary.txt ...
Read 81 entries from D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt/summary.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Adding fc.raw.file column ... done
Reading file D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt/proteinGroups.txt ...
Read 1183 entries from D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt/proteinGroups.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Reading file D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt/evidence.txt ...
WARNING: Could not find column regex '^fraction$' using case-INsensitive matching.
WARNING: Could not find column regex '[RK].Count' using case-INsensitive matching.
WARNING: Could not find column regex '^protein.names$' using case-INsensitive matching.
Keeping 25 of 60 columns!
Read 254391 entries from D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt/evidence.txt.
[1] "While checking ID column: last ID was 'NA', while table has '254391' rows."
Error in get(x, envir = this, inherits = inh)(this, ...) :
Error: file 'D:/R/mydirectory/Shenghuahao/maxquant-result/combined/txt/evidence.txt' seems to have been edited in Microsoft Excel and has artificial line-breaks which destroy the data at lines (roughly): 1
Please fix (e.g. try LibreOffice 4.0.x or above)!"

This is a regression from:
#10

The error occurs in v0.80.3 when dropping a file(!) from with a txt folder with spaces anywhere in the path.
The error does not occur when drag'n'dropping the folder itself.

Installation PTXQC console second attempt.pdf
Installation PTXQC console.pdf

I tried installation from 2 different cran mirror sites. Seems like PTXQC was not installed. Please help finishing the installation.

Thank you,

Sjef

PS Also the help server gives an error:

...but should be searched in the protein ID as well.

Currently, the user would see a 'contaminant ... not found in any sample' instead of the plot they are looking for.

Also, when proteingroups.txt is not available, the protein id from evidence.txt should be used as a fallback.

Thanks to Oana for reporting!

(the order should be reversed from left to right)

probably due to some change within newer versions of ggplot2.

Hi Chris,
It could be useful to add the top 5 modifications (similar to the top 5 contaminants) for those who use the 'dependent peptides' option. Is that possible?
Kind regards,
Sjef

As suggested by a reviewer, it would be great to import and track meta information, such as

• instrument operator
• acquisition date
• change of LC column (should be visible without meta data, but you never know)
• ...

in the report (maybe side-by-side with the heatmap) -- or even via comparing a heatmap clustering (by rows) to any of these factors.

To ease burden on the user to enter the data, one could use a Raw file naming scheme template (regex with named groups?),

Raw file: “QExactive01_CB_20141123_SampleXY….raw”
with scheme

(?<machine>.*)_(?<op>.*)_(?<date>.*)

Hi Chris,

I use the drag_n_drop batch file on a Windows machine and it used to work just fine. However, we hava one Maxquant run where we can't get a report after draging the txt folder on to the batch file.

I attach a screen shot of the log file so you can see what it happening. The weird thing about it is that other maxquant folders in the same directory run through and a report is created. And I can not see what is different about this one so that the error occurs.

Maybe you can see what's going on and have an idea how we can fix this.

Thanks
saskia

Hi Chris,

I managed to install PTXQC without any problems on my Mac and could create a QC report by connecting to the corresponding txt folder on the network drive, all good.
But when I try to install it on a Windows machine, the install_github command fails.
Here ist what I get and my session info:

install_github("cbielow/PTXQC", build_vignettes = TRUE)
Downloading GitHub repo cbielow/PTXQC@master
Installing PTXQC
"C:/PROGRA1/R/R-321.3/bin/x64/R" --no-site-file --no-environ --no-save
--no-restore CMD build
"C:\Users\sas\AppData\Local\Temp\RtmpcJf0s1\devtoolsfb0406e3de6\cbielow-PTXQC-96df116"
--no-resave-data --no-manual

• checking for file 'C:\Users\sasrei\AppData\Local\Temp\RtmpcJf0s1\devtoolsfb0406e3de6\cbielow-PTXQC-96df116/DESCRIPTION' ... OK
• preparing 'PTXQC':
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ...Warning: running command '"C:/PROGRA1/R/R-321.3/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
  ERROR
  Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc is not available. Please install both.
  Warning in readLines(con) :
  incomplete final line found on 'PTXQC-Basic_Guide_for_R_users.Rmd'
  Error: processing vignette 'PTXQC-Basic_Guide_for_R_users.Rmd' failed with diagnostics:
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because PTXQC-Basic_Guide_for_R_users.Rmd appears to be an R Markdown v2 document.
  Execution halted
  Error: Command failed (1)

session_info()
Session info -----------------------------------------------------------------------------------------------------
setting value
version R version 3.2.3 (2015-12-10)
system x86_64, mingw32
ui Rgui
language (EN)
collate English_Australia.1252
tz Australia/Sydney
date 2016-01-18

Packages ---------------------------------------------------------------------------------------------------------
package * version date source
Biobase * 2.30.0 2015-10-14 Bioconductor
BiocGenerics * 0.16.1 2015-11-06 Bioconductor
BiocInstaller 1.20.1 2015-11-18 Bioconductor
curl 0.9.4 2015-11-20 CRAN (R 3.2.3)
devtools * 1.9.1 2015-09-11 CRAN (R 3.2.3)
digest 0.6.9 2016-01-08 CRAN (R 3.2.3)
httr 1.0.0 2015-06-25 CRAN (R 3.2.3)
knitr 1.12 2016-01-07 CRAN (R 3.2.3)
magrittr 1.5 2014-11-22 CRAN (R 3.2.3)
memoise 0.2.1 2014-04-22 CRAN (R 3.2.3)
R6 2.1.1 2015-08-19 CRAN (R 3.2.3)
stringi 1.0-1 2015-10-22 CRAN (R 3.2.3)
stringr 1.0.0 2015-04-30 CRAN (R 3.2.3)

I tried installing pandoc but got the same error afterwards.
Any hints?

Thanks a lot
cheers
satz

Hi Chris,
I have encountered an error just as tile say, in this case, I have 206 sample in together to analyze, how to configure it out? Thanks!
R version 3.2.3 (2015-12-10), windows 7 system, 64 bit

require(PTXQC)
Loading required package: PTXQC
Loading package PTXQC (version 0.80.0)
txt_folder = "D:/R/mydirectory/PTXQC/shenhuahao-103/txt"
r = createReport(txt_folder)
getYAML with: PTXQC$UseLocalMQPar default: TRUE
.. return default: TRUE
getYAML with: PTXQC$ReportFilename$extended default: TRUE
.. return default: TRUE
meta id: qcMetric_PAR
getYAML with: order$qcMetric_PAR default: 1
.. return default: 1
meta id: qcMetric_PG_PCA
getYAML with: order$qcMetric_PG_PCA default: 3
.. return default: 3
meta id: qcMetric_EVD_Top5Cont
getYAML with: order$qcMetric_EVD_Top5Cont default: 10
.. return default: 10
meta id: qcMetric_PG_Ratio
getYAML with: order$qcMetric_PG_Ratio default: 19
.. return default: 19
meta id: qcMetric_EVD_UserContaminant
getYAML with: order$qcMetric_EVD_UserContaminant default: 20
.. return default: 20
meta id: qcMetric_EVD_PeptideInt
getYAML with: order$qcMetric_EVD_PeptideInt default: 30
.. return default: 30
meta id: qcMetric_PG_RawInt
getYAML with: order$qcMetric_PG_RawInt default: 32
.. return default: 32
meta id: qcMetric_PG_LFQInt
getYAML with: order$qcMetric_PG_LFQInt default: 33
.. return default: 33
meta id: qcMetric_PG_ITRAQInt
getYAML with: order$qcMetric_PG_ITRAQInt default: 34
.. return default: 34
meta id: qcMetric_MSMS_MissedCleavages
getYAML with: order$qcMetric_MSMS_MissedCleavages default: 40
.. return default: 40
meta id: qcMetric_EVD_Charge
getYAML with: order$qcMetric_EVD_Charge default: 100
.. return default: 100
meta id: qcMetric_PG_Cont
getYAML with: order$qcMetric_PG_Cont default: 110
.. return default: 110
meta id: qcMetric_MSMSScans_TopNoverRT
getYAML with: order$qcMetric_MSMSScans_TopNoverRT default: 120
.. return default: 120
meta id: qcMetric_EVD_IDoverRT
getYAML with: order$qcMetric_EVD_IDoverRT default: 150
.. return default: 150
meta id: qcMetric_EVD_RTPeakWidth
getYAML with: order$qcMetric_EVD_RTPeakWidth default: 170
.. return default: 170
meta id: qcMetric_EVD_MBRAlign
getYAML with: order$qcMetric_EVD_MBRAlign default: 210
.. return default: 210
meta id: qcMetric_EVD_MBRIdTransfer
getYAML with: order$qcMetric_EVD_MBRIdTransfer default: 220
.. return default: 220
meta id: qcMetric_EVD_MBRaux
getYAML with: order$qcMetric_EVD_MBRaux default: 221
.. return default: 221
meta id: qcMetric_MSMSScans_IonInjTime
getYAML with: order$qcMetric_MSMSScans_IonInjTime default: 240
.. return default: 240
meta id: qcMetric_EVD_MS2OverSampling
getYAML with: order$qcMetric_EVD_MS2OverSampling default: 250
.. return default: 250
meta id: qcMetric_EVD_PreCal
getYAML with: order$qcMetric_EVD_PreCal default: 260
.. return default: 260
meta id: qcMetric_EVD_PostCal
getYAML with: order$qcMetric_EVD_PostCal default: 270
.. return default: 270
meta id: qcMetric_MSMS_MSMSDecal
getYAML with: order$qcMetric_MSMS_MSMSDecal default: 280
.. return default: 280
meta id: qcMetric_SM_MSMSIdRate
getYAML with: order$qcMetric_SM_MSMSIdRate default: 300
.. return default: 300
meta id: qcMetric_MSMSScans_TopN
getYAML with: order$qcMetric_MSMSScans_TopN default: 350
.. return val: 120
meta id: qcMetric_MSMSScans_TopNID
getYAML with: order$qcMetric_MSMSScans_TopNID default: 380
.. return default: 380
meta id: qcMetric_EVD_PeptideCount
getYAML with: order$qcMetric_EVD_PeptideCount default: 400
.. return default: 400
meta id: qcMetric_EVD_ProteinCount
getYAML with: order$qcMetric_EVD_ProteinCount default: 450
.. return default: 450
meta id: qcMetric_AverageQualOverall
getYAML with: order$qcMetric_AverageQualOverall default: 9999
.. return default: 9999
getYAML with: File$Parameters$enabled default: TRUE
.. return default: TRUE
Reading file D:/R/mydirectory/PTXQC/shenhuahao-103/txt/parameters.txt ...
Read 61 entries from D:/R/mydirectory/PTXQC/shenhuahao-103/txt/parameters.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Starting to work on PAR: MQ Parameters ...
... PAR: MQ Parameters done
getYAML with: PTXQC$NameLengthMax_num default: 10
.. return default: 10
getYAML with: File$Summary$enabled default: TRUE
.. return default: TRUE
Reading file D:/R/mydirectory/PTXQC/shenhuahao-103/txt/summary.txt ...
Read 413 entries from D:/R/mydirectory/PTXQC/shenhuahao-103/txt/summary.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Adding fc.raw.file column ... done
getYAML with: File$Summary$IDRate$Thresh_bad_num default: 20
.. return default: 20
getYAML with: File$Summary$IDRate$Thresh_great_num default: 35
.. return default: 35
Starting to work on SM: MS^2 ID rate (">%1.0f") ...
... SM: MS^2 ID rate (">%1.0f") done
getYAML with: File$ProteinGroups$enabled default: TRUE
.. return default: TRUE
getYAML with: File$ProteinGroups$RatioPlot$LabelIncThresh_num default: 4
.. return default: 4
Reading file D:/R/mydirectory/PTXQC/shenhuahao-103/txt/proteinGroups.txt ...
Read 1287 entries from D:/R/mydirectory/PTXQC/shenhuahao-103/txt/proteinGroups.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
getYAML with: File$ProteinGroups$IntensityThreshLog2_num default: 25
.. return default: 25
Starting to work on PG: Contaminants ...
... PG: Contaminants done
Starting to work on PG: raw intensity ...
... PG: raw intensity done
Starting to work on PG: LFQ intensity ...
... PG: LFQ intensity done
Starting to work on PG: Principal Component ...
... PG: Principal Component done
getYAML with: File$Evidence$enabled default: TRUE
.. return default: TRUE
getYAML with: File$Evidence$ProteinCountThresh_num default: 3500
.. return default: 3500
getYAML with: File$Evidence$IntensityThreshLog2_num default: 23
.. return default: 23
getYAML with: File$Evidence$PeptideCountThresh_num default: 15000
.. return default: 15000
Reading file D:/R/mydirectory/PTXQC/shenhuahao-103/txt/evidence.txt ...
Requiring column(s) 'retention.length' to be of type 'numeric'!
Requiring column(s) 'retention.time.calibration' to be of type 'numeric'!
Requiring column(s) 'retention.time', 'calibrated.retention.time' to be of type 'numeric'!
Requiring column(s) 'match.time.difference' to be of type 'numeric'!
Requiring column(s) 'intensity' to be of type 'numeric'!
Requiring column(s) 'mass.error..ppm.', 'mass.error..da.', 'uncalibrated.mass.error..ppm.', 'uncalibrated.mass.error..da.' to be of type 'numeric'!
Requiring column(s) 'uncalibrated...calibrated.m.z..ppm.', 'uncalibrated...calibrated.m.z..da.' to be of type 'numeric'!
Requiring column(s) 'm.z' to be of type 'numeric'!
Requiring column(s) 'score' to be of type 'numeric'!
WARNING: Could not find column regex '^fraction$' using case-INsensitive matching.
WARNING: Could not find column regex '[RK].Count' using case-INsensitive matching.
Requiring column(s) 'charge' to be of type 'numeric'!
Requiring column(s) 'mass' to be of type 'numeric'!
Requiring column(s) 'ms.ms.count' to be of type 'numeric'!
Keeping 17 of 62 columns!
Read 1214661 entries from D:/R/mydirectory/PTXQC/shenhuahao-103/txt/evidence.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Adding fc.raw.file column ... done
getYAML with: File$Evidence$SpecialContaminants default: c("MYCOPLASMA", "1")
.. return default: c("MYCOPLASMA", "1")
Starting to work on EVD:Contaminant (%s) ...
... EVD:Contaminant (%s) done
Starting to work on EVD: Pep Intensity (">%1.1f") ...
... EVD: Pep Intensity (">%1.1f") done
Starting to work on EVD: Prot Count (">%1.0f") ...
... EVD: Prot Count (">%1.0f") done
Starting to work on EVD: Pep Count (">%1.0f") ...
... EVD: Pep Count (">%1.0f") done
Starting to work on EVD: RT Peak Width ...
... EVD: RT Peak Width done
getYAML with: File$Evidence$MQpar_MatchingTimeWindow_num default: 1
.. return default: 1
getYAML with: File$Evidence$MatchBetweenRuns_wA default: auto
.. return default: auto
Starting to work on EVD: MBR Align ...
... EVD: MBR Align done
Starting to work on EVD: MBR ID-Transfer ...
... EVD: MBR ID-Transfer done
Starting to work on EVD: MBR auxilliary ...
... EVD: MBR auxilliary done
Starting to work on EVD: Charge ...
... EVD: Charge done
Starting to work on EVD: ID rate over RT ...
... EVD: ID rate over RT done
getYAML with: File$Evidence$MQpar_firstSearchTol_num default: 20
.. return default: 20
getYAML with: File$Evidence$firstSearch_outOfCalWarnSD_num default: 2
.. return default: 2
Starting to work on EVD: MS Cal-Pre (%1.1f) ...
... EVD: MS Cal-Pre (%1.1f) done
getYAML with: File$Evidence$MQpar_mainSearchTol_num default: NA
.. return default: NA
Starting to work on EVD: MS Cal-Post ...
... EVD: MS Cal-Post done
Starting to work on EVD: Contaminants ...
... EVD: Contaminants done
Starting to work on EVD: MS^2 Oversampling ...
... EVD: MS^2 Oversampling done
getYAML with: File$MsMs$enabled default: TRUE
.. return default: TRUE
Reading file D:/R/mydirectory/PTXQC/shenhuahao-103/txt/msms.txt ...
Requiring column(s) 'missed.cleavages' to be of type 'numeric'!
Requiring column(s) 'evidence.id' to be of type 'numeric'!
Keeping 2 of 60 columns!
Read 1257721 entries from D:/R/mydirectory/PTXQC/shenhuahao-103/txt/msms.txt.
Updating colnames
Simplifying contaminants
Simplifying reverse
Adding fc.raw.file column ... done
Starting to work on MSMS: MS^2 Cal (%s) ...
... MSMS: MS^2 Cal (%s) done
Starting to work on MSMS: %s ...
... MSMS: %s done
getYAML with: File$MsMsScans$enabled default: TRUE
.. return default: TRUE
Reading file D:/R/mydirectory/PTXQC/shenhuahao-103/txt/msmsScans.txt ...
Requiring column(s) 'ion.injection.time' to be of type 'numeric'!
Requiring column(s) 'retention.time' to be of type 'numeric'!
Keeping 2 of 63 columns!
Error : cannot allocate vector of size 125.0 Mb
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Error:

Parsing the file 'D:/R/mydirectory/PTXQC/shenhuahao-103/txt/msmsScans.txt' failed. See message above why. If the file is not usable but other files are ok, disable the corresponding section in the YAML config. You might also be running a foreign locale (e.g. Chinese) - switch to an English locale and make sure that txt files are encoded in ASCII (Latin-1)!

Hi,
trying to intsall PTXQC as a noob, i try the Drag 'n Drop method. Following all the instructiosn i'm stuck at the following error:

"Quitting from lines 33-60 (PTXQC-Basic_Guide_for_R_users.Rmd)
Error: processing vignette 'PTXQC-Basic_Guide_for_R_users.Rmd' failed with diagnostics:
could not find function "guides"
Execution halted
Error: Command failed (1)"

what is going wrong?

some pointers here:
https://www.mcponline.org/content/5/4/652

The corresponding QualScore tool is available in TPP, but not maintained since its publication...

Is there an example how to use the app?
When I do

browseVignettes(package = 'PTXQC')
I get

Error in unlist(str_split(x, "\n"), recursive = FALSE, use.names = FALSE): lazy-load database '/home/.../miniconda3/envs/py3/lib/R/library/stringr/R/stringr.rdb' is corrupt
Traceback:

Hello,
I was able to use PTXQC with some classical (HCD MS2 at high resolution) iTRAQ data acquired on a Fusion instrument. But when I use a multinotch method (MS2 CID at low resolution for identification, MS3 HCD at high resolution for reporter quantification, = Reporter ion MS3 in MaxQuant), PTXQC crashes when processing the data. Both classical and multinotch data were processed on the same computer with drag and drop setup. MaxQuant version is 1.5.3.30.
Error-message.txt

Reason: MaxQuant 1.2 uses 'BasePeak Intensity' as column name in msmsscans.txt, whereas MaxQuant 1.3+ use 'Base Peak Intensity'.

Workaround for affected PTXQC versions:
set

    enabled: no

in the .yaml file

the error message looks like this:

... MS^2*Scans: Ion Inj Time  done
Starting to work on MS^2*Scans: Intensity ...
Warning in .self$checkInput(c("fc.raw.file", "total.ion.current", "base.peak.intensity"),  :
  Input check failed: columns 'base.peak.intensity' are not present in input data!
 Show Traceback
 
 Rerun with Debug
 Error: .self$checkInput(c("fc.raw.file", "total.ion.current", "base.peak.intensity"),  .... is not TRUE

Hello there! Thanks for your quick replay in #55...

Now, I having a problem with the analysis of the information from 'evidence' file. In fact, the information of this file is missing when I ran the analysis over the entire 'txt' folder. see attached the 'evidence' file I am using and the report from PTXQC... see below the error...

Starting to work on EVD: Reporter intensity ...
Error in data.table(df_reps) :
"data.table" fucntion not found

let me know if you need other info...

thanks in advance... your help is really appreciated...

Mario

report_v0.92.6.log
evidence.txt

Hi, I am a PTXQC user from China, there is some problem in installing PTXQC in my laptop.

The R version is 3.2.3

The command is as follows:

if (!require(devtools, quietly = TRUE)) install.packages("devtools")
library("devtools")
source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
biocLite("Biobase")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) ‘Biobase’
试开URL’https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/Biobase_2.30.0.zip'
Content type 'application/zip' length 4227858 bytes (4.0 MB)
downloaded 4.0 MB

package ‘Biobase’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Administrator\AppData\Local\Temp\Rtmpe8h2Nd\downloaded_packages

install_github("cbielow/PTXQC", build_vignettes = TRUE)
Downloading GitHub repo cbielow/PTXQC@master
Installing PTXQC
"C:/Program Files/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD build
"C:\Users\Administrator\AppData\Local\Temp\Rtmpe8h2Nd\devtoolsf081956398e\cbielow-PTXQC-96df116" --no-resave-data
--no-manual

Hi everybody,
I've been using the DragNdrop version of PTXQC because I'm too bad in R.
For the first time I have the message "Duplicated input given to "shortenString"" and the program stops.
I have attached an image of the error and the MQ .txt files.
I'm I posting in the right place of this is just for experienced R users?

Thank you in advance.
All the best,
Paola

parameters.txt
report_v0.92.4.log

mzRange.txt

summary.txt

tables.pdf
proteinGroups.txt

Oxidation (M)Sites.txt

I installed R in a conda environment and started a jupyter notebook with an R-kernel. When I try to install PTXQC I get the following:

install.packages("PTXQC")

also installing the dependencies ‘curl’, ‘httr’, ‘rvest’, ‘kableExtra’

Warning message in install.packages("PTXQC"):
“installation of package ‘curl’ had non-zero exit status”Warning message in install.packages("PTXQC"):
“installation of package ‘httr’ had non-zero exit status”Warning message in install.packages("PTXQC"):
“installation of package ‘rvest’ had non-zero exit status”Warning message in install.packages("PTXQC"):
“installation of package ‘kableExtra’ had non-zero exit status”Warning message in install.packages("PTXQC"):
“installation of package ‘PTXQC’ had non-zero exit status”Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

Any ideas why the packages cannot be installed?

Occurs in v0.80.1 and later when computing the missing values metric for a MaxQuant run consisting of only one Raw file.

I'm trying to use the LCSn function with the following function call:

LCSn(c("AAAAACBBBBB", "AAAAADBBBBB", "AAAABBBBBEF", "AAABBBBBDGH"))

I was expecting the results to be either "BBBBB" or at least "AAA" however what is returned is "".

Thank you!

Thanks for developing this nice software. I have installed the latest version (v0.82.1) of PTXQC at the environment of R 3.3.2. It is running fine except a larger data set (~200 raw files). There it stopped right after working on EVD: Pep Missing Values and no PDF/Html reports generated.

The message looks like this:
Starting to work on EVD: MS^2 Oversampling ...

Memory [MB] prior|after|max(diff) : 2707.2 | 2707.4 | 5362.7 (2656)

Duration: 10 s

... EVD: MS^2 Oversampling done
Starting to work on EVD: Pep Missing Values ...
Error in array(STATS, dims[perm]) : 'dims' cannot be of length 0
Press any key to continue . . .

What could be the problem? If this step makes problem, could we skip this step and report only others that have passed through?

Downloading GitHub repo cbielow/PTXQC@master
from URL https://api.github.com/repos/cbielow/PTXQC/zipball/master
Installing PTXQC
"C:/Users/Vogel_lab/R-3.2.1/bin/x64/R" --no-site-file --no-environ --no-save
--no-restore --quiet CMD build
"C:\Users\Vogel_lab\AppData\Local\Temp\Rtmp0ap5qF\devtools2908543220d1\cbielow-PTXQC-7c4baff"
--no-resave-data --no-manual

• checking for file 'C:\Users\Vogel_lab\AppData\Local\Temp\Rtmp0ap5qF\devtools2908543220d1\cbielow-PTXQC-7c4baff/DESCRIPTION' ... OK
• preparing 'PTXQC':
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ...Warning: running command '"C:/Users/VOGEL_1/R-321.1/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
  ERROR
  Error: processing vignette 'PTXQC-Basic_Guide_for_R_users.Rmd' failed with diagnostics:
  package 'yaml' not found
  Execution halted
  Error: Command failed (1)

this should allow the user to spot weird mass offsets (from unidentified PTMs or non-peptide signals)

(mentioned in #25)

Plots derived from proteinGroups.txt (like the PCA plot) currently do not benefit from shortened Raw file names (via ), since experimental groups not necessarily correspond 1:1 to Raw files (its a n:m mapping).

We could, however, obtain the mapping from evidence.txt ('raw file' and 'experiment' column) and allow for manual editing in the report_v0.xyz_filename_sort.txt by adding three more columns

• experiment (original)
• experiment (short/display) <-- editable
• experiment (best effort)

ProteinGroups whose name starts with either L, M, or H will not be shown in the respective plots from source "PG", due to a wrong RegEx.

Hi PTXQC team,
I tried to test PTXQC for the MaxQuant output of Bruker's TimsTOF raw data. Unfortunately it failed to generate any result. I have attached the log file for your review.
I have a feeling this may not be an easy fix. I am wondering if you have any plans to expand your valuable PTXQC for the TimsTOF data that is gaining popularity.
Thanks
Hossein

report_v0.92.3.log

Thank you for this wonderful QC software. I do see a few possibilities for improvement though.
I like the Match Between runs plots very much. But, sometimes there are no graph’s in the “EVD: alignment” check page. A remark appears: Could not find a unique reference Raw file even though the data in the Evidence table seem okay. Changing “MatchBetweenRuns_wA” from auto to yes did not help. Can the software be changed to just show the data in the Evidence table?
Another issue that needs changes has to do with the injection naming. Short names nor best effort names are taken over in the PCA plots, PG: (LFQ) intensity distribution plots and PG: Contaminant per condition plot. Can it be changed to show the short name?

Thank you very much,

Sjef Boeren

report_v0.80.7_combined.pdf
evidence.txt

Hello! I am trying to run an analysis with PTXQC. The thing is when I try to analyze the entire 'txt' folder this error comes up:

... MSMS: MS^2 Cal (%s) done
Starting to work on MSMS: %s ...
Error in !df_msms$contaminant : invalid argument
Also: Warning message:
Using alpha for a discrete variable is not advised

could you please help me?

see attached the msms files I am currently using...

thanks in advance!

Mario
msms_files.zip

Hi!
I used the PTXQC previously without problems. Now on a new machine, somehow I am not able to make it run. Any ideas what did I do wrong this time?

This batch file is used to invoke the QC script by drag'n'dropping of
a MaxQuant txt folder (or any file within) onto this .bat file.
Within the same txt folder, a QC report in Html/PDF format will be created.

First time installation of this script [for admins only]:
The script expects a certain structure to be present.
This .bat file expects a subfolder named '_internal'
which holds:
'R-3.1.0' Holds a complete R installation
(including all packages required to run the
PTXQC package)
'compute_QC_report.R' The R script that is invoked by this .bat
Found QC directory at 'Z:\B_Rawfiles\Hek_Hela\QC-dragdrop\_internal'
-- 'Z:\Witek\Projects\20191111-SCX_Marco\MQ-txt' is a directory
Txt folder is at 'Z:\Witek\Projects\20191111-SCX_Marco\MQ-txt'
Found R at '"Z:\B_Rawfiles\Hek_Hela\QC-dragdrop\_internal"\R-3.1.0\bin\x64\rscr
ipt.exe'.
Using YAML file and calling R now ...
Calling '"Z:\B_Rawfiles\Hek_Hela\QC-dragdrop\_internal"\R-3.1.0\bin\x64\rscript
.exe --vanilla "Z:\B_Rawfiles\Hek_Hela\QC-dragdrop\_internal"\compute_QC_report
.R Z:\Witek\Projects\20191111-SCX_Marco\MQ-txt '
Error: package or namespace load failed for 'PTXQC':
.onLoad failed in loadNamespace() for 'pillar', details:
call: utils::packageVersion("vctrs")
error: there is no package called 'vctrs'
Execution halted
Failed folder Z:\Witek\Projects\20191111-SCX_Marco\MQ-txt. Does it exist and is
writeable!?

The error should be indicated above.
Common errors are (yours might be different)

• your R installation runs out of memory; especially if its 32bit
• the file 'Z:\B_Rawfiles\Hek_Hela\QC-dragdrop\_internal\compute_QC_report.R'
  is missing

If the error persists, follow the
instructions on https://github.com/cbielow/PTXQC
in the section 'Bug reporting'.

Leave this window open until the bug report is submitted

You can copy the text from this window by

1. right-clicking here
2. choose 'Select all'
3. press the 'Enter' key
4. paste it somewhere (issue ticket, email)
   This ensures that all text is available to debug the problem.
   Thanks!
   Press any key to continue . . .`

Hi PTXQC team,

during the report generating the following error message appeared:

While loading MQ data: shortened raw filenames are not unique! This should not happen. Please contact the developers and provide the above names!

Adding fc.raw.file column ...Original names:
3265_Lumik3_Shakya_150IS_HCD_11A_1 3265_Lumik3_Shakya_150IS_HCD_11B_1 3265_Lumik3_Shakya_150IS_HCD_11C_1 3265_Lumik3_Shakya_150IS_HCD_11D_1 3265_Lumik3_Shakya_150IS_HCD_12A_1 3265_Lumik3_Shakya_150IS_HCD_12B_1 3265_Lumik3_Shakya_150IS_HCD_12C_1 3265_Lumik3_Shakya_150IS_HCD_12D_1 3265_Lumik3_Shakya_150IS_HCD_13A_1 3265_Lumik3_Shakya_150IS_HCD_13B_1 3265_Lumik3_Shakya_150IS_HCD_13C_1 3265_Lumik3_Shakya_150IS_HCD_13D_1 3265_Lumik3_Shakya_150IS_HCD_14A_1 3265_Lumik3_Shakya_150IS_HCD_14B_1 3265_Lumik3_Shakya_150IS_HCD_14C_1 3265_Lumik3_Shakya_150IS_HCD_14D_1Short names:
........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1 ........_1Error in res(x, ...) :

version 0.92.4 not working
version 0.90.0 working
MQ version 1.6.2.10

Thanks for support
Kind regards
Kamil Mikulasek

Proteomics Core Facility and Zbynek Zdrahal Research Group
CEITEC-MU
Masaryk University

Each plot (or set of plots) could be annotated with some descriptive text and the scoring function which is derived from the data shown to produce the heatmap.
This is probably more convenient to do for the HTML report.

Following installation procedure as described (R-3.2.3; 64 bit), the first test of PTXQC resulted in attached error message. If required I can send MaxQuant txt folder via wetransfer.

• txt folder exists and is writeable
• R is 64 bit
• compute_QC_report.R is present
• directory structure is present as described in installtion procedure

Hi,

I have issues installing the package. I am following the very helpful installation documentation and after installing PTXQC it returns

The downloaded binary packages are in
        C:\Users\reviewer3\AppData\Local\Temp\RtmpwbY4zy\downloaded_packages

This folder does not contain '\PTXQC\inst\QC-dragdrop'. Is there anything I can do to get unstuck?

Btw with (let's call it ) I guess you mean (let's call it <QCdir>).

Thanks!

when PTXQC found custom contaminants (e.g. mycoplasma), but not all Raw files are above threshold,
an error will be generated

 Show Traceback
 
 Rerun with Debug
 Error in FUN(X[[i]], ...) : 
  getTitles() for EVD:Contaminant~(%s): No title found in ggplot object at index 2! 

This leads to an empty report.

Hi Chris,

sorry to be a pain but I updated to the newest version and tried the same folder that was acting up before but I get the same error. I tried the dragndrop and the R script.
Here I attach the error from the R script with all packages I loaded.
Maybe I screwed something else up, or is it the data itself?

Thanks again
Saskia