lt;- if(l2FCShrink){ as.data.frame(lfcShrink(dds, contrast=rn, type = "ashr")); } else { as.data.frame(results(dds, contrast=rn)); } results.df$log2FoldChange <- round(results.df$log2FoldChange, 2); results.df

We have RNAseq data with 4 cell lines with different knockout genotypes (WT, A, G, GA), and for each cell lines, we have two treatment types: treated (H) and untreated (C) with 5 replicates for each condition. we are interested in the treatment effect on each of these cell lines: WT.H_C, A.H_C, G.H_C, or GA.H_C (H_C means treatment vs untreat comparison). These are easily to be done in DESeq2 bas…

me 1618. This only happens if I use lfcShrink with "apeglm". It doesn't happen with "normal" or "ashr" or if I just use "results". Attached is an example of my code and also my ColData for dds1. Due to sequencing issues, I have some