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Posts by snatanf
Comment: C: DESeq2 standalone TE usage
... I think I see your point that it doesn't matter if the SizeFactors for ctrl_RNASeq counts (SF_ctrl_RNA) and ctrl_RiboSeq (SF_ctrl_Ribo) normalize the the ctrl counts to 1M or some other number, however it seems to me that it is critical that the SizeFactor ratio: (SF_ctrl_RNA)/(SF_ctrl_Ribo) remai ...
... Hi, I am new DESeq2 user, interested in Translation Efficiency (TE) and Log2FoldChange (L2FC) of TE. To the best of my understanding, before DESeq2 calculates TE (RiboSeq/RNASeq), the counts are normalized with the appropriate SizeFactor. The SizeFactors take into account the geometric avg of count ...
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