gongx030 / drimpute Goto Github PK

Dear author,

Thanks for developing the software! I have a few questions but did not find clear answer from your paper:

1. is the input a count matrix?
2. is the output a count matrix? Has it been normalized by library size, or log2-transformed?
3. I tried to use a raw count matrix as an input, but find in output matrix almost all values are very small (1e-2)?

Thanks!

I was trying to set mc.cores = 16, but it reported not supporting 'mc.cores' >1.
How to fix it?

Hello,

I'm trying to run DrImpute and had some issues.

First, running on R 3.5.3, preprocessSC and preprocess are not recognized as functions:

Error in preprocessSC(camp_counts, min.expressed.gene = 0) : 
  could not find function "preprocessSC"

I've tried it on R 3.4.3 (based on Readme sessioninfo) and got exactly the same output.

Second, the DrImpute function seems to be failing to run. When I run it, I get the following output:

> X.imp <- DrImpute(X.log)
[2019-05-09 00:50:03] number of cells: 21086
[2019-05-09 00:50:03] number of genes: 26774
[2019-05-09 00:50:08] % zero events (X=0): 92.8%
[2019-05-09 00:50:09] % robustly expressed events (X>5): 0.3%
[2019-05-09 00:50:09] fast imputation: FALSE

This output is followed by an eternal loading. I've allowed it to run for over 18 hours in our HPC cluster (128GB RAM, 16 cores) and couldn't have it running. I don't think this is a memory or processing issue, since we've already performed more demanding tasks in this HPC, such as alignment and massive dataset merging.

Any chance we can get an update?

Hi,

I tried to run DrImpute on the expression profiles of 50k single cells and 7596 genes. It seems DrImpute failed when dealing with long vectors. May I have your help check it? Thanks!

Error:

[2019-08-22 15:49:48] number of cells: 50000
[2019-08-22 15:49:48] number of genes: 7596
[2019-08-22 15:49:56] % zero events (X=0): 80.4%
[2019-08-22 15:49:57] % robustly expressed events (X>5): 5.1%
[2019-08-22 15:49:57] fast imputation: FALSE
Error in Ds[[i]] <- as.matrix(1 - cor(X, method = "spearman")) : 
long vectors not supported yet: ../.././R-3.5.1/src/include/Rinlinedfuns.h:519
Calls: DrImpute -> getCls
Execution halted

Dear @gongx030 ,

I have been trying to install your imputation package in R without success. I get the following error:

libRblas.so: cannot open shared object file: No such file or directory

I've tried different 'solutions' posted online (e.g. https://groups.google.com/forum/#!msg/rapache/axLb5PsS9LY/7ZkP831LULkJ or http://promberger.info/linux/2009/03/20/r-lme4-matrix-not-finding-librlapackso/), but they haven't worked for me.

I am working under the following session:

R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_GB.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] devtools_1.13.5

loaded via a namespace (and not attached):
[1] httr_1.3.1 compiler_3.4.4 R6_2.2.2 tools_3.4.4 withr_2.1.2 curl_3.2 yaml_2.1.18 memoise_1.1.0 git2r_0.21.0 digest_0.6.15

Thanks a lot in advance for your help!

These files prevent the package from being installed correctly using install_github, and should not be included. Once the files were removed in my clone, I was able to successfully install the package (R 3.4.3, Scientific Linux 7).