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seoanezonjic / ExpHunterSuite

RNA-seq gene expression analysis suite
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Functional hunter doesn't work #14

Closed JoseCorCab closed 4 years ago

JoseCorCab commented 4 years ago

Functional Hunter is not working. In case of no-wgcna execution, it breaks during markdown template execution giving this error

Quitting from lines 354-419 (functional_report.Rmd) Error in fc_readable(x, foldChange) : objeto 'geneList' no encontrado Calls: <Anonymous> ... cnetplot -> cnetplot -> cnetplot.enrichResult -> fc_readable

When launching wgcna it return this error: Error in download.KEGG.Path(species) : 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'... Calls: lapply ... prepare_KEGG -> download_KEGG -> download.KEGG.Path

It seems that the program is not recognicing the species name

Here you have a test dataset with both cases: https://www.dropbox.com/s/magsd6yjgffv52y/issue_test.zip?dl=0

fmjabato commented 4 years ago

About geneList bug, I see that you are not running GSEA enrichments and "geneList" is generated only for GSEA modules. I'll check the report, thank you for info.

About KEGG error, I need, at least, "control_treatment.txt" to use your test data and I assume that you're using Git biomaRt_organism_table.txt file and not a custom one.

Please, give me the control_treatment file to reproduce your error

fmjabato commented 4 years ago

Okey, your reported bugs have been fixed:

  1. "geneList" bug consist on report assuming that geneList always exists, but only is calculated when GSEA module has been launched. Now, geneList is always calculated
  2. KEGG errors occurs for "clusters" mode and consists on an undesired launch of "remote" mode even if remote mode has not been requested.

After that, I close this issue