Normalized counts to be used in decoupleR from deseq2 results
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James • 0
@f1538197
Last seen 4 weeks ago
United States

So, to run the Univariate linear model(Ulm), you need the normalized counts. Using your example, you used the normalized log-transformed counts. In deseq2, would that be equivalent to retrieving this information from this code:

counts(dds, normalized = TRUE)

I hope that makes sense.

decoupleR • 432 views
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@james-w-macdonald-5106
Last seen 6 hours ago
United States

No, you never use normalized counts for anything but plotting. Can you point out the example that uses normalized counts?

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