g:profiler not running

[risserlin]

Ran random example on g:profiler website, download GEM file, plugged into EM

Cytoscape 3.9.1, EM 3.3.4

[mikekucera]

I used the GEM file as an 'enrichments' file and it worked.

Can you please provide more detailed steps to reproduce, because I may be missing something, or send me the GEM file you used. Thanks.

[risserlin]

gProfiler_hsapiens_6-24-2022_10-24-58 AM.gem.txt

[mikekucera]

It works. Ruth, this fails for you?

[Julia-Elsayed-Moustafa]

Hello, I have been trying to use EnrichmentMap 3.3.4 in Cytoscape 3.9.1.

I have been using a gem file generated from my own data using gProfiler in R (code used -taken from the gProfiler tutorial- included below):

Produce GEM table for cytoscape

gem <- gostres$result[,c("term_id", "term_name", "p_value", "intersection")] colnames(gem) <- c("GO.ID", "Description", "p.Val", "Genes") gem$FDR <- gem$p.Val gem$Phenotype = "+1" gem <- gem[,c("GO.ID", "Description", "p.Val", "FDR", "Phenotype", "Genes")] head(gem, 3)

write.table(gem, file = "MM_gProfiler_gem_20220907.txt", sep = "\t", quote = F, row.names = F)

GMT file downloaded from the following link (https://biit.cs.ut.ee/gprofiler/static/gprofiler_full_hsapiens.ENSG.gmt).

I get the following error anytime I try to run EnrichmentMap:

Index 1 out of bounds for length 1.

Any idea what mimght be causing this?

Thanks!

[risserlin]

Can you send me a sample of your MM_gProfiler_gem_20220907.txt file?

How are the genes in the "Genes" column separated?

[Julia-Elsayed-Moustafa]

example.gem.txt

Hello, I've attached an example file with the first few lines. They are comma separated (I fed in the standard output I got from gProfiler).

[risserlin]

It works for me.

What version of cytoscape and Enrichment map are you using?

[Julia-Elsayed-Moustafa]

Hm, ok, thanks, I'll keep trying to reinstall everything... I'm using EnrichmentMap 3.3.4 in Cytoscape 3.9.1.

[risserlin]

I am using 3.3.4 snapshot. It is possible that I might be using the later version than the one released. Let me downgrade to the released version to check.

[risserlin]

Yes. It works with the released version as well. Does the example file that you sent me work for you?

Maybe it is something in the full file that is causing problems.

[Julia-Elsayed-Moustafa]

I actually just re-installed Cytoscape and EnrichmentMap again (same versions), and the full file has now started working, no change in file itself or versions installed. No idea what caused the issue over the last few days, but glad it's now working! Thanks very much for your quick replies.