**30**wrote:

Hello there,

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?

Any advice?

Many thanks!!!