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Difference in total normalized counts for replicates - DeSeq2

Hello,

I have extracted the normalised counts for my RNAseq samples using Deseq2 with standard recommended command

dds <- estimateSizeFactors(dds)
counts(dds, normalized=TRUE)

However, when I sum up the total number of normalised counts per sample, I am seeing a differences in the latter for replicates. For example, sample A1 total = 40 million, whereas A2 total = 50 million. Is this normal? Why are they so different?

Thanks for any help you can provide.

rna-seq deseq2
• 2,956 views • link
written by urmi208 • urmi208

FYI, that won't be identical, just in the same vague range.

• 1 views • link
written by Devon Ryan Devon Ryan

2 answers

I don't know what variable you are using, but you didn't assign the normalised counts to anything. I guess you want something like:

normcounts <- counts(dds, normalized=TRUE)
• 1 views • link
written by WouterDeCoster WouterDeCoster

Yes, that's correct. Sorry I missed that.

• 1 views • link
written by urmi208 • urmi208

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