Biosets should be filtered by lfc>1.2, not 1.5

R-ODAF / R-ODAF_Health_Canada

Health Canada's version of the R-ODAF pipeline, which includes additional visualization and pipelining features

MIT License

2 stars 3 forks source link

Biosets should be filtered by lfc>1.2, not 1.5 #204

Closed LMBradford closed 5 months ago

LMBradford commented 5 months ago

We currently filter for biosets output using params$linear_fc_filter, which is set to 1.5 (setupd_functions.R, lines 116 and 121). That's the right filter for filtering DEGs, but for Chris Corton (EPA)'s biosets analysis, the filter should be 1.2.

Need to hard-code that into DESeq_functions.R lines 273, 275.