Hi,

I would to have a data frame with normalized counts of my RNA-seq data set. I used DESeq2 to analyse these data.

This is the code I used to generate normalized counts :

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition)

dds <- DESeq(ddsHTSeq)

table_counts_normalized <- counts(dds, normalized=TRUE)

But I see here [DESEQ2] How to access the normalized data of a DESeqDataSet that we can do :

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition)

dds <- estimateSizeFactors(ddsHTSeq)

table_counts_normalized <- counts(dds, normalized=TRUE)

Which is the good solution ?

Thanks a lot for your answer !

Joanna

These give the same output but the second is faster because it skips dispersion estimation and GLM fitting which is not necessary to compute the size factors.