This is the first time I've tried to import Kallisto output using tximport for use in DESeq2. I want to get the sizeFactors calculated by DEseq2 and use them for normalizating counts from another experiment. But I am only able to get size factors for each gene individually (normalizationFactors(dds)), and not each library combined. Should I compute the mean for each column or something like that?

Thanks, Jon

The column mean of normalization factors will be something like the size factor, yes.

If you want the size factors just as they are computed by DESeq2, you can do the following:

normMatrix <- assays(dds)[["avgTxLength"]]
normMatrix <- normMatrix / exp(rowMeans(log(normMatrix)))
sf <- estimateSizeFactorsForMatrix(counts(dds) / normMatrix)