DESeq2 : normalized counts
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JoannaF ▴ 10
@joannaf-9881
Last seen 9 weeks ago
France

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

rnaseq deseq2 normalized counts • 4.8k views
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@mikelove
Last seen 22 hours ago
United States

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.

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Thanks a lot !!

Joanna

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