Dear All, The data set has 3 controls, and 9 treatments (transgenic biological replicates with different levels of gene expression), we use DESeq (multi-factor design) to normalize the raw data for math. modeling. How to use the output from DESeq to convert the raw read counts (integers) to normalized data (decimals) ?? What do you think the data normalized using DESeq is good for math. modeling ? Thanks Xin Davis NCSU [[alternative HTML version deleted]]

Hi Xin On 2012-05-11 18:14, Xin Davis wrote: > The data set has 3 controls, and 9 treatments (transgenic biological > replicates with different levels of gene expression), we use DESeq > (multi-factor design) to normalize the raw data for math. modeling. How to > use the output from DESeq to convert the raw read counts (integers) to > normalized data (decimals) ?? "counts( cds, normalized=TRUE )" gives you the normalized counts (i.e., raw counts, divided by size factors, to account for differences in sequencing depth) > What do you think the data normalized using DESeq is good for math. > modeling ? You will need to elaborate on what you mean by "math. modeling" to allow us to answer this question. And have a look at the section on the variance-stabilizing transformation in the DESeq vignette, in case this is what you are looking for. Simon