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Posts by adam
... 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 ...
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. ...
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