New cummeRbund user here! I'm trying to extract a list of differentially expressed genes from a CuffSet, but I'm finding that the values displayed in the sigMatrix plot do not match those given to me by getSig(). For example, when comparing sampleX and sampleY in the sigMatrix, it shows 101 significant genes at alpha= 0.05. However, getSig() tells me there are 140 in the same CuffSet for the same alpha value.
Any ideas for what could account for this discrepancy? If I make sure that sigma always equals 0.05, shouldn't I be getting the same number of significantly differentially expressed genes?
Code:
>A <- readcufflinks(dir=system.file(“data”, package=”cummerbund”)) >A CuffSet instance with: 6 samples 23284 genes 30073 isoforms 25872 TSS 24748 CDS 348555 promoters 388080 splicing 305730 relCDS > sigMatrix(A, level=’genes’, alpha =0.05) >length(getSig(A, alpha=0.05, x= ‘sampleX’, y= ‘sampleY’)) [1] 140