I'm new to R and Limma, so apologies in advance for my naivete.
I'm analyzing some microarray data, and after applying the BH correction w/ topTable, I end up with a list of genes where the adj. P-value is apparently all the same. How do I interpret that? The P-values (unadjusted) vary significantly, but the ad. P-value for each gene is the same number (0.2800681 in my case).
I also note that some of my top results are labeled as normgene->intron (aka not real genes). Could this be the issue? I used the oligo package for initial processing of my data.
Any guidance would be much appreciated.