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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
Quang
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10
Thank you ATpoint for linking the resource. Could I just clarify that so even if we do `~ Date_lysed + Subset * Conditions` in which `Date_…
Answer: DESeq2 analysis with transcript counts
by
ATpoint
★
4.6k
You need to account for the inferential uncertainty of mapping, that is because transcripts of the same gene shared most exonic content, so…
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
▴
10
Hi, James. I forgot to mention, but yes, I did run `DESeq2::DESeq()`. So, I ran `DESeq2::DESeqDataSetFromHTSeqCount`, then `DESeq2::DESeq()…
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