Normalisation in DESeq2

@bine-23912

Last seen 8 days ago

Dear all,

For my exploratory analysis I used the vst function to normalise my data.
But I read that it is not necessary for the Differential Expression via DESeq2 since it has already a build-in normalisation on the data, is this correct?
I read it in this article I believe: S. A. Michael I. Love 2019:RNA-seq workflow: gene-level exploratory analysis and differential expression

Also I understood that for the statistical analysis the raw counts and not the normalised values should be used?

Thank you,
Bine

DESeq2
Normalization
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7 weeks ago • updated 6 weeks ago
Bine
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@mikelove

Last seen 2 days ago

United States

Yes that is correct:

"There are two separate paths in this workflow; the one we will see first involves transformations of the counts in order to visually explore sample relationships. In the second part, we will go back to the original raw counts for statistical testing. This is critical because the statistical testing methods rely on original count data (not scaled or transformed) for calculating the precision of measurements."

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Thank you very much :)