Normalizing Salmon output count data matrix using DESeq2
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kiqbal • 0
@7cabb0d9
Last seen 4 weeks ago
United States

I import counts and abundance matrix from Salmon output using tximport. I want to normalize the Salmon output count matrix using DESeq2 package. What code should I use to achieve this task? Can I do similar with Abundance output of Salmon?

Thank you

DESeq2 tximport counts Salmon • 155 views
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@mikelove
Last seen 3 hours ago
United States

Do you mean scale the counts for sequencing depth?

dds <- DESeqDataSetFromTximport(txi, ~condition)
ncts <- counts(dds, normalized=TRUE)

The abundance isn't something that DESeq2 operates on (e.g. statistics are made from counts alone).

If you want to scale TPM using a similar procedure of median-ratio, you can manually calculate TPM size factors with estimateSizeFactorsForMatrix.

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