**0**wrote:

I have four genes in four rows in a matrix. The `results`

function of the DESeq2 calculated the baseMean of the four row as

37.6, 2071.5, 1.0, 491.6

But if I calculate the means with rowMeans(counts(dds,normalized=TRUE)), then I get

45.2, 2679.8, 1.0, 491.6

Why is this happen?

And when I calculate the base mean per level with

baseMeanPerLvl <- sapply( levels(dds$condition), function(lvl) rowMeans( counts(dds,normalized=TRUE)[,dds$condition == lvl] ) )

which was posted on this forum by Michael Love, and I calculate the log2 fold change, then I get a different value then it is calculated by the `results`

function.

**19k**• written 16 months ago by asd •

**0**