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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 5 months ago by ★ 4.5k • written 5 months ago by • 0
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Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 870
If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …
Comment: ANOVA like approach of edgeR by SamGG ▴ 350
Simply remove the cell type from the model. design <- model.matrix(~targets$Status)
Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870
You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…
Answer: Identical samples after deseq2 batch effect removal by maripane • 0
Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0
The updated version worked well on my data. Thank you!
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