**230**wrote:

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