MaayanLab / enrichr_issues

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[BUG] Export entries to table with background genes has wrong stats #66

Closed ycl6 closed 1 month ago

ycl6 commented 1 year ago

Hi,

When running enrichment analysis on the EnrichR website with background genes, the results showing on the web and those provided in the exported TXT file are not the same. Those on the web has the correct stats, whereas those in the exported TXT file are stats analysed without background genes.

Below shows the results from GO Molecular Function 2023 when I use the examples provided on the website:

Results copied from the web, when analysed without background genes

Index | Name | P-value | Adjusted p-value | Odds Ratio | Combined score
-- | -- | -- | -- | -- | --
4 | fatty-acyl-CoA Binding (GO:0000062) | 0.001626 | 0.3190 | 15.82 | 101.58
6 | Acyltransferase Activity, Transferring Groups Other Than Amino-Acyl Groups (GO:0016747) | 0.006961 | 0.3190 | 4.48 | 22.26

Results copied from the web, when analysed with background genes

Index | Name | P-value | Adjusted p-value | Odds Ratio | Combined score
-- | -- | -- | -- | -- | --
1 | fatty-acyl-CoA Binding (GO:0000062) | 0.0003711 | 0.1004 | 27.12 | 214.19
2 | Acyltransferase Activity, Transferring Groups Other Than Amino-Acyl Groups (GO:0016747) | 0.001135 | 0.1004 | 6.93 | 47.01

Results in the exported TXT file, when analysed with background genes

Term    Overlap P-value Adjusted P-value    Old P-value Old Adjusted P-value    Odds Ratio  Combined Score  Genes
fatty-acyl-CoA Binding (GO:0000062) 3/13    0.0016262077325928145   0.3190301517265964  0   0   15.818548387096774  101.57887995484002  ALDH6A1;ACBD4;SCP2
Acyltransferase Activity, Transferring Groups Other Than Amino-Acyl Groups (GO:0016747) 5/64    0.006960657855853012    0.3190301517265964  0   0   4.48144754924416    22.261506851119684  LIPT1;OSGEPL1;SCP2;ZDHHC5;MCAT
jeevangelista commented 1 month ago

Hi I think this is fixed. Closing this now.