So here is a dumb question for someone like me who forgot her high school math. I've seen in papers that they cut by two fold a log2 fold change in RNA-seq data. So let's say that I have 5 up regulated genes like in the table above, if I cut by two fold, does it mean that I only keep log2 fold changes that are higher than 2?
Gene log2fold
A 5.00
B 4.00
C 3.00
D 1.55
E 1.00
Just as a side comment, ranking genes and setting a cut-off on logFC tends to include mostly genes expressed at low levels. This is because statistically and maybe also biologically, low expressed genes tend to have larger differences.
Conversely, ranking and filtering by FDR tends to favour genes expressed at high levels.
A workaround this is to select genes that are towards the perifery of the cloud of the MAplot (i.e. plot of expression vs logFC). I wrote a little R script to do this (intensityFilter.R).