I have posted this on biostars but this is the more appropriate forum to ask this question (apologies if you have seen this already).
I am running an enrichment analysis on 3000 differentially expressed genes (mouse) following DESeq2.
The pwf plot for upregulated genes (log2FoldChange > 0) is similar to the one in the vignette, with long genes being more differentially expressed.
However, the plot for significantly downregulated genes is inverted. High proportion of short genes that are DE and low proportion of long DE genes.
If I plot all DE expressed genes no sensible line can be dawn as the bins cancel each other out (high scatter, poor fit). I have seen quite a few of these graphs when searching for "pwf plot goseq" on google including some on the bioconductor forum - but as yet there is no explanation for this.
Any ideas why this might be?
When I manually bin the deseq2 results by baseMean I do not get a difference in for downregulated (=FALSE) vs upregulated (=TRUE) genes.
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