Hi all,

I am now using raw reads to calculate the differential gene expression. I see DESeq gives SizeFactors for each sample and can use that for normalization. But it seems DESeq only use that normalization for visualization, not for calculate the differential pvalue. Is that correct?

I've read DESeq paper and still not very clear about that. I know DESeq use NB distribution to calculate the pvalue. But for raw reads, it must be normalized first, right?? Thanks,

Che

Thanks a lot Steve. I may make a mistake. Is the sizeFactors the only normalization method used in DESeq? After the sizeFactors normalization, can the value be used for fold-change detection between two samples?

Have you read the DESeq vignette? Fold changes are calculated for you after a call to

`nbinomTest`

, for example. To just get something like a matrix of expression that you can calculate fold changes for data exploration, look at the example in section 6, where they shoot their data through a variance stabilizing transformation.