How to get normalized count table from DESeq?

How to get normalized count table from DESeq?

1

Hi,

I’m using Deseq compare differential abundance. Here is my code:

ds.all <- phyloseq_to_deseq2(ps0.infant.pbs, ~ sample_type)

geoMeans <- apply(counts(ds.all),1,gm_mean)

ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans)

dds.all <- DESeq(ds.all,fitType = "local")

Then as the results I got 8 ASVs that showed significantly different.

My questions:

  1. I used geoMeans is because otherwise DESeq() would fail with error:

     Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  : 
    

    every gene contains at least one zero, cannot compute log geometric means

    So does that mean these two steps:

   geoMeans <- apply(counts(ds.all),1,gm_mean) 

   ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans)

are normalization steps of DESeq? Or there are other hidden normalization steps in DESeq?

  1. How can I extract the normalized count table that DESeq used to generate the 8 ASVs? I tried counts(ds.all), but the count table is exactly the same with the raw count table.

  2. I also tried counts(dds, normalized=T), it does look like a normalized count table, but how can I know if this is the exact normalized count table that deseq used for its analysis?

Thanks!
Leran


DESeq

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