updated 7.2 years ago by
koneill
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written 7.3 years ago by
kelly.joanne.andrews
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Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
by
Nicholas
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0
Got it, so using the GTF directly rather than any of the annotation packages will yield more accurate results than any of the packages? I g…
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
by
James W. MacDonald
67k
I agree that it's difficult to match an `EnsDb` object to the build, but I think that is orthogonal to OP's issue, which is mapping transcr…
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
Quang
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10
I see. Thank you for your advice!
In my case per James' suggestions, I redesigned the model to `~ DonorID + Subset + Conditions` as Date_…
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
by
ATpoint
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4.6k
> that you should stick with whatever IDs you started with,
Meaning, you got your fasta file for the kallisto index from somewhere, e.g. …
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
Michael Love
43k
Think of two separate paths in DESeq2: 1) visualization/EDA and 2) testing.
For (1) you use vst(), removeBatchEffect(), etc. The design is…
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