getSig and sigMatrix in CummeRbund

[jfarr]

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.

>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

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?