[BioC] How to use DESeq output to convert raw counts to normalized data

[Simon Anders]

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