**70**wrote:

Hi,

according to my script here below, why DESEq2 calculations and my own are not identical? What am I missing?

Any halp will be most welcome, thanks.

David

dds<- makeExampleDESeqDataSet(n=100,m=18)

dds <- DESeq(dds, betaPrior = FALSE)

resultsNames(dds)

res <- results(dds)

res[1,2]

# [1] -0.3811565

my.log2FoldChange <- log(rowMeans(counts(dds[,10:18],normalized=TRUE))[1]/rowMeans(counts(dds[,1:9],normalized=TRUE))[1],2)

my.log2FoldChange

# -0.3792306

res[1,3]

# [1] 0.2197007

my.lfcSE <- sd(log(counts(dds[1,10:18],normalized=TRUE)/counts(dds[1,1:9],normalized=TRUE),2))/sqrt(8)

# [1] 0.2036169

**26k**• written 3.1 years ago by David Rengel •

**70**