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  • getSig and sigMatrix in CummeRbund

    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.

    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
    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?

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