jmw86069 / splicejam Goto Github PK

Hello,
testing the jamGeomean() function on a vector containing NaN, it returns NaN although na.rm is set to TRUE.

small example

x = c(-3, 5, -4, 0, 4, -1, -2, 3, 2, -5, NaN)
jamGeomean(x, na.rm = TRUE)
[1] NaN

Hi, I am using your great software want to call differential splicing.
However, when i reached here, there was a problem:
diffSpliceL <- runDiffSplice(
iMatrixTx=iMatrixTxTPM,
detectedTx= detectedTx,
tx2geneDF=tx2geneDF,
txColname=txColname,
geneColname=geneColname,
iDesign=iDesign,
iContrasts=iContrasts,
cutoffFDR=0.05,
cutoffFold=1.5,
collapseByGene=TRUE,
spliceTest="t",
verbose=FALSE,
useVoom=FALSE);

Saying: Error in iMatrixTx[detectedTxUse, , drop = FALSE] : subscript out of bounds
How can i solve them?

I use mouse as species, i followed your pipeline, all is well, only one part when i do
geneMatch <- match(rownames(txiTx[[assayNames[1]]]),
tx2geneDF[,txColname]);
It seems the order is chaotic, so i use this following instead.
assays1=lapply(txiTx[assayNames], function(x){log2(1+x)})
rowData1=DataFrame(tx2geneDF[geneMatch,,drop=FALSE])
colData1=DataFrame(sampleDF)
rownames(rowData1) <- NULL
TxSE <- SummarizedExperiment(
assays=assays1,
rowData=rowData1,
colData=colData1,
);

This "rownames(rowData1) <- NULL" is what i add.

Bad Gateway as of 2 PM March 16. 😢

I get error messages when installing Splicejam. This error was unexpected because I successfully used Splicejam a month ago. However, a month later, I got error messages each time I wanted to load the package. In an attempt to solve the problem, I uninstalled splicejam and tried reinstalling again, but keep getting error messages. I am using two platforms, one having R version 3.6 and the other having R version 4:

The following error was generated from version 4.0
Error: Failed to install 'splicejam' from GitHub:
Failed to install 'jamba' from GitHub:
(converted from warning) installation of package ‘C:/Users/Bruker/AppData/Local/Temp/RtmpU38hNU/file2b684a8e33e6/jamba_0.0.55.900.tar.gz’ had non-zero exit status

For R version 3.6, the following version was generated:
make: *** [cpp11.o] Error 1
ERROR: compilation failed for package ‘tidyr’

• removing ‘/home/relindis/R/x86_64-redhat-linux-gnu-library/3.6/tidyr’
  Error: Failed to install 'splicejam' from GitHub:
  (converted from warning) installation of package ‘tidyr’ had non-zero exit status

I really appreciate any help that can enable me successfully install and load splicejam.
Thank you