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Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
by
Nicholas
•
0
Just an update on this: I tried ```tximport``` with ```tx2gene``` objects from the three annotation packages and from the GTF file itself. …
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
by
Nicholas
•
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
▴
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
★
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. …
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