Hi,

I want to extract the normalized the data matrix (reads matrix) to do differential gene expression analysis by myself instead of using wald test the package provided as I don't have replicates in each comparison group. so, there is no statistical calculation but only fold change between two samples. I am going to use vsn normalized matrix to do this work. My question is what is the advantages and drawbacks of using normalized data matrix instead of using the raw counts? What datamatrix (count) should be appropriate for this type analysis.

Thank you

-W

The fold changes calculated by DESeq(), either the moderated (default) or unmoderated fold changes (using addMLE or betaPrior=FALSE), will not be the same as the ones obtained from rlog or VST data. The moderated fold changes are calculated as described in the paper. The unmoderated fold changes in a simple group comparison are equal to (if you allow some pseudo latex):

mean_{j in group B}(K_ij / s_j) / mean_{j in group A}(K_ij / s_j)

Got it, I think so. Thank you Michael. -W