I am a little confused by the toptable output (well really the FDR) and thought I'd quickly check my interpretation.
For the following code:
topall <- toptable(fit, coef="CaseAD", genelist=fit$genes, number=Inf, adjust="fdr", p.value=0.01, lfc=log2(1))
Would the interpretation be:
Using a threshold of 0.05 for FDR adj. p.values and a minimal fold change of 2, this analysis produces n number of genes?
And does the above mean that I would look at the adjusted p.values?
I am interested in following MAQC guidelines for this analysis, so would rather restrict my results to a FDR = 0.05 and p.values < 0.01. However, I am not entirely sure, how to get that, since I am not sure what the "adjust=fdr" relates to here?