Differential IR Analysis (GLM) Issue

[viktor-hub]

I'm trying to conduct a differential IR analysis by following the Wiki example (https://github.com/williamritchie/IRFinder/wiki/Generalized-Linear-Model-with-Replicates).

The files filePaths.txt and experiment.txt have 3 WT samples and 3 KO samples.

When I get to the step metaList=DESeqDataSetFromIRFinder(filePaths=paths, designMatrix=experiment, designFormula=~1), I receive the following error:

[1] "processing file 1 at /home/PathToWTSample-1/IRFinder-IR-dir.txt"
[1] "processing file 2 at /home/PathToWTSample-2/IRFinder-IR-dir.txt"
[1] "processing file 3 at /home/PathToWTSample-3/IRFinder-IR-dir.txt"
[1] "processing file 4 at /home/PathToKOSample-1/IRFinder-IR-dir.txt"
[1] "processing file 5 at /home/PathToKOSample-2/IRFinder-IR-dir.txt"
[1] "processing file 6 at /home/PathToKOSample-3/IRFinder-IR-dir.txt"
Error in dimnames(x) <- dn :
  length of 'dimnames' [1] not equal to array extent

I would appreciate any advice, and thank you so much for IRFinder!

[dg520]

Hi @viktor-hub ,

I guess you're using IRFinder 1.2.6. And I'm sorry there is a bug in the DESeq2Constructor.R. A quick fix is to change Line 22 in the R script From

tmp6=max(tmp4,tmp5)

to

tmp6=pmax(tmp4,tmp5, na.rm=T)

And re-run from the beginning of the tutorial.

Alternatively, you can re-download IRFinder 1.2.6 from GitHub, as I've updated both the source code and the release.

I sincerely apologize for this terrible mistake.

Best, Dadi

[viktor-hub]

Thank you!