User: adam

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order of factors
... Hi Micheal, I am trying to understand the directionality of the log2 fold change that is reported by DESeq2.   I see in the manual that it says that the first level of the factor will be taken as the dominator for calculations by DESeq2.  I also see that the order of the factor levels matters when ...
deseq2 written 2.7 years ago by adam0 • updated 2.7 years ago by Michael Love23k
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Answer: A: Batch correction in DESeq2
... I believe the "counts" function in DESeq2 will provide the type of normalization you you looking for.  Make sure to use the "normalized=TRUE" flag.   ...
written 2.9 years ago by adam0

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