I used different tools to do differently expressed genes analysis. From the results I see a general difference in logFC values for genes from limma-voom, edgeR and DESeq2. Although some people saw difference in logFC between edgeR and EDSeq2 and got good answers, in my case edgeR and DESeq2 get very simmilar results but quite different from limma-voom.
I found that (not sure, i saw it somewhere)
limma's logFC =mean(log2(Group1))-mean(log2(Group2))
Actual logFC= log2(mean(Group1)/mean(Group2))
Can this small difference in famulars cause a general big difference in limma-voom with other tools(edgeR and DESeq2) ?
Which logFC is better to trust?
Below is a figure of the comparison of different logFCs