Changing the direction of logfold change?

Question

[Sharon]

I would like to understand if the last line in my code does need the negative sign. Like when to use etp$table$logFC = -etp$table$logFC and when to ignore this line. I saw some tutorials adding this which changes the direction of the results and this confuses me. I am testing normal samples vs. tumor samples

group <- c(rep("ctrl", 10), rep("tr", 10))
dge = DGEList(counts=data, genes= rownames(data), group=group)

countsPerMillion <- cpm(dge)
summary(countsPerMillion)
countCheck <- countsPerMillion > 1
summary(countCheck)
keep <- which(rowSums(countCheck) >= 2)
dge <- dge[keep,]
summary(cpm(dge))

dge <- calcNormFactors(dge, method="TMM")
dge <- estimateCommonDisp(dge)
dge <- estimateTagwiseDisp(dge)

et <- exactTest(dge, pair=c("ctrl", "tr"))
etp <- topTags(et, n=2000000)
etp$table$logFC = -etp$table$logFC

Thanks a lot

[russhh]

What do you want the logFC values to look like: do you want positive signs if there is higher expression in the treatment than the control? I wouldn't include that final line, I'd modify your line where et is defined: pair = c('ctrl', 'tr') should give the reflection of pair = c('tr', 'ctrl'). Look into the help page for exactTest to determine what order you should present your groups

Answer 1

[Devon Ryan]

Yes that will change to sign of the fold-change. The only reason to do this would be if you misspecified things in exactTest(). As a rule, I would strongly encourage people to not go around swapping the sign on their fold-changes without a very good reason.

[Sharon]

Thank you all. Much appreciated. So if I have pair set to pair (control, tumor) and I removed this line (etp$table$logFC = -etp$table$logFC), then if I found in the results a negative logfold change, then that would mean the control is more expressed than the tumor? and if I found a postive sign foldchange, then this means the tumor is more expressed than the control. Am I correct? Thanks

[Devon Ryan]

Yes, that's correct.

[Sharon]

Thanks, much appreciated