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bzhanglab / WebGestaltR

R package for WebGestalt
https://bzhanglab.github.io/WebGestaltR/
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Warning when loading reference gene list #3

Closed Pweidemueller closed 1 year ago

Pweidemueller commented 5 years ago

Dear zhanglab, I get following warning when doing an Overrepresentation analysis with a gene list and a custom reference gene list. using WebGestaltR. When the reference list is loaded, following warning flashes:

Loading the functional categories... Loading the ID list... Loading the reference list... data length [43707] is not a sub-multiple or multiple of the number of rows [10929]

I can't make sense of that warning, because when I ran the exact same analysis before I did not get it. Can I just ignore it? I still get enrichment results, but when I run the analysis online on your web applet 1. no warning flashes and 2. the results differ from the ones returned by WebGestaltR. So I'm unsure if I can trust the analysis right now.

I attach the gene list and reference gene list. THis is the code I used:

WebGestaltR(interestGeneFile= allSpecies_CorrelatingGenes_Testis.txt, interestGeneType="ensembl_gene_id", enrichMethod="ORA", organism="hsapiens", enrichDatabase="geneontology_Biological_Process_noRedundant", referenceGeneFile=allSpecies_ReferenceGenes_Testis.txt, referenceGeneType="ensembl_gene_id", fdrMethod="BH", # Benjamini Hochberg sigMethod="fdr", fdrThr=0.01, isOutput=TRUE,outputDirectory="Extract_PeakGenes/Biological_Process", projectName=allSpecies)

I appreciate any help! allSpecies_ReferenceGenes_Testis.txt allSpecies_CorrelatingGenes_Testis.txt

yxngl commented 5 years ago

I tried with the latest version and it seems fine. Could you try to update to the latest version from CRAN?