[BioC] How to use DESeq output to convert raw counts to normalized data
anders at embl.de
Fri May 11 18:46:07 CEST 2012
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
> 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
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