Dear all,

In DESeq2, DESeq2 used the median of ratios for normalization count, instead of CPM and TPM I have three replication for EMT and EWT. Is it possible to average EMT1,2,3 to represent one normalization count number?

Thanks in advance

Best regards,

crossed post:https://www.biostars.org/p/9468094/

DESeq2 doesn't have functionality to create averages but you can do it yourself easily with: rowMeans, indexing [,] and counts(dds, normalized=TRUE).