Hi,
I tried to filter out genes with a count less than 2.0, and it seems that the lowest padj value for these genes is 1.350968e-44, and that removing these genes reduces the number of DE genes. Is this possible or have I done something wrong?
I tried to filter out genes with a count less than 2.0, and it seems that the lowest padj value for these genes is 1.350968e-44, and that removing these genes reduces the number of DE genes. Is this possible or have I done something wrong?
Code:
> filterTreshold = 2.0 > keep = rowMeans(counts(ddsHTSeq, normalized=TRUE)) > filterTreshold > table(keep) keep FALSE TRUE 8007 13673 > min(res$padj[!keep], na.rm=TRUE) [1] 1.350968e-44 > table(p.adjust(res$pvalue, method="BH") < .1) FALSE TRUE 17870 2610 > table(p.adjust(res$pvalue[keep], method="BH") < .1) FALSE TRUE 11285 1645
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