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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
James W. MacDonald
67k
How you analyze your data is up to you. But do note that Subset * Conditions implies that you want to find genes that respond to stimulus d…
Comment: MBDseq analysis using qsea package
by
kf
•
0
Hi Matthias,
Happy new year! I wondered if it is possible to retrieve normalized value from each samples? makeTable seems only return beta…
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
Quang
•
0
Hi, James. I forgot to mention, but yes, I did run `DESeq2::DESeq()`. So, I ran `DESeq2::DESeqDataSetFromHTSeqCount`, then `DESeq2::DESeq()…
Answer: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
ATpoint
★
4.6k
It's an FAQ in the vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-s…
Comment: Deseq2, enrichGO and ensembl ID
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James W. MacDonald
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I am not sure I understand. You say that a unique Ensembl ID maps to multiple gene symbols. That doesn't mean you have two genes (it's just…
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