Hi all,

I have different libraries of NGS and want to use DESeq to normalize them. I want to make the count comparable among different libraries, but how can I get the normalized count (in integer number but not float value)?

In the DESeq mannual, there is code like this:

cds <- newCountDataSet( countsTable, conds )

cds <- estimateSizeFactors( cds )

cds <- estimateVarianceFunctions( cds )

res <- nbinomTest( cds, "T", "N")

And about the normalization, I have sample1,2,3, each sample only has one replicate, if I want to compare sample1 and 2, should I normalize between 1 and 2, while if to compare 2 and 3, then again normalized between 2 and 3? Can I normalize sample 1,2,3 together then compare 1,2 or 2,3?

Thanks!

I have different libraries of NGS and want to use DESeq to normalize them. I want to make the count comparable among different libraries, but how can I get the normalized count (in integer number but not float value)?

In the DESeq mannual, there is code like this:

cds <- newCountDataSet( countsTable, conds )

cds <- estimateSizeFactors( cds )

cds <- estimateVarianceFunctions( cds )

res <- nbinomTest( cds, "T", "N")

And about the normalization, I have sample1,2,3, each sample only has one replicate, if I want to compare sample1 and 2, should I normalize between 1 and 2, while if to compare 2 and 3, then again normalized between 2 and 3? Can I normalize sample 1,2,3 together then compare 1,2 or 2,3?

Thanks!

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