Hi all,
I'm working on RNAseq data set and use DESeq2 in order to find differentially expressed genes above a given log2FoldChange, say 2 (or -2 for downregulated genes), by simply using R to filter all results above 2 and below -2, respectiely. I performed this analysis according to manual and everything worked well two weeks ago.
Today I ran the script again with same parameters and same input, but I got different result, e.g. I found a higher number of upregulated genes compared to the run two weeks ago. When I check for given genes in my old and new results I can see that baseMean is still the same but log2FoldChangechanged.
I can also see that lcfSE was always below 1 in my two week-old results, but now its in above 1 in most cases.
I saw that a new version of DESeq2 was released some days ago.
Now my question: Was statistical computation of l2fc somehow altered? I can simply not figure out why my results differ... Looking forward to your answers!
Best regards
Andi