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fallerlab / ARF

Differential Ribosomal heterogeneity Prediction through Ribosome Profiling generated rRNA fragments and their Proximity to Ribosomal Proteins
GNU General Public License v3.0
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Error: replacement has length zero with test samples #4

Closed jason2389 closed 1 year ago

jason2389 commented 1 year ago

Hello, I am running the script with the test samples and I am getting this error:

preparing geneSet collections... GSEA analysis... leading edge analysis... done... Error in x[[jj]][iseq] <- vjj : replacement has length zero

R version 4.2.1

Thanks for your help!

ferhatalkan commented 1 year ago

Hi, sorry to hear about the issue. Can you specify in which function do you get the error? If possible, can you copy/paste the exact command as well?

jason2389 commented 1 year ago

I get the error after the the leading edge analysis

GSEA analysis... leading edge analysis... done... Error in x[[jj]][iseq] <- vjj : replacement has length zero

dripARF_results <- ARF::dripARF(samplesFile = "Rpl10aRps25Rpl22_samples_mouse.tsv", organism="mm", QCplot=TRUE, targetDir="dripARF_results/")

Thanks!

ferhatalkan commented 1 year ago

Just figured out the reason, it is because of clusterProfiler::GSEA function now returns a column with ID "qvalue" not "qvalues" as ARF expecting. I can release a fix accepting both ids, but, Can you let me know which version of clusterProfiler you are using so that I can make sure this is the problem?

ferhatalkan commented 1 year ago

Also the version of DOSE package?

jason2389 commented 1 year ago

That would be great if you could release an updated version!

DOSE package : 3.22.1 clusterProfiler : 4.4.4

ferhatalkan commented 1 year ago

If you don't want to wait for the new release (I need to do some tests etc. , so, it might take a bit since I'm adding a few other fixes), you can clone the git repository to your local machine, change the "qvalues" to "qvalue" at line 440, 450 and 1060 within ARF_platform.R script and install from your updated repository. Let me know if that works :)

ferhatalkan commented 1 year ago

The change at line 440 might not be needed though.

jason2389 commented 1 year ago

Thanks for the info. I have created a branch and did the changes you suggested. Now it works! Many thanks!

nayanvs commented 1 year ago

I used the cloned version to avoid qvalues errors with the test data but ran into another error with it. Waiting for the new release.

No id variables; using all as measure variables Error in base::nchar(wide_chars$test, type = "width") : lazy-load database '/usr/local/lib/R/site-library/cli/R/sysdata.rdb' is corrupt In addition: Warning message: In base::nchar(wide_chars$test, type = "width") : internal error -3 in R_decompress1

ferhatalkan commented 1 year ago

This looks more like a package installation error. Also seems like it comes from another package, not from ARF.