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
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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Just out of curiosity, what type of normalization is applied by the "counts(dds, normalized=TRUE)" statement? I mean, is there a specific name for this normalisation? I want to know about the mathematics behind this. Thank you.
Median ratio scaled counts. Read the DESeq2 paper for the median ratio calculation.
If you are using tximport, note that we use a different approach, described in tximport paper.
Thank you for the reference. Also, if I am using tximport and then normalising the counts, at the backend the normalising (which is specific to counts from tximport, as you mentioned is different) is automatically taken care of? Right?
Yes, tximport --> DESeq2 corrects for sequencing depth in addition to gene length.