User: ATpoint
ATpoint • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Germany
- Website:
- https://www.biostars.o...
- Last seen:
- 1 day, 10 hours ago
- Joined:
- 2 years ago
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- a*********@gmail.com
Wet-lab biologist by training, wannaba computational biologist.
Biostars Mod: ATpoint
Posts by ATpoint
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Comment:
C: Problem in featureCounts file.
... Cross-posted: https://www.biostars.org/p/392402/ ...
written 21 days ago by
ATpoint • 10
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... Your samples notably cluster by cell line, not by treatment. Therefore it appears unfortunate to use them as biological replicates. From a biological standpoint this quite normal for cell lines. During cell line establishment there are a lot of things changing inside the cell, particular clones star ...
written 6 weeks ago by
ATpoint • 10
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... I think you need a design formula without intercept `(~0 + ...)` see edgeR manual (https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf) p.69 section 4.4.6 ...
written 6 weeks ago by
ATpoint • 10
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... What do you find opposing? As PCA is typically the first step in quality control and detection of potential batch effects, one typically sets it to `T` to get a blinded/unbiased view on the data. ...
written 6 weeks ago by
ATpoint • 10
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... The [InTAD paper][1] states `InTAD can be applied to any heterogeneous cohort of samples analyzed by a combination of gene expression and epigenetic profiling techniques and integrates either public or custom information of TAD boundaries.` What I am missing is a statement on its application on non- ...
written 7 weeks ago by
ATpoint • 10
• updated
7 weeks ago by
Konstantin Okonechnikov • 20
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... Just for the record, I suggested to cross-post this question here at BioC which originally was posted at [Biostars][1] a few weeks ago.
[1]: https://www.biostars.org/p/370025/#381520 ...
written 12 weeks ago by
ATpoint • 10
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... Thank you both for the outstanding responsiveness to questions and issues. Can you move Aaron's comment to answer so it is the toplevel answer? ...
written 3 months ago by
ATpoint • 10
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... Maybe add a short comment to the `tximport` vignette referencing the suggestions from Aaron below. Using the corrected counts for things like clustering etc. is standard so I was actually surprised no one asked this before (by best knowledge, maybe I missed the respective threads). ...
written 3 months ago by
ATpoint • 10
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... Cross-posted on [Biostars][1] as suggested by Aaron.
[1]: https://www.biostars.org/p/379520/ ...
written 3 months ago by
ATpoint • 10
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... Thanks Aaron,
I think that should do it. If you move your comment to answer I can accept it.
For completeness, here is the code I used:
## convert DGElist to SummarizedExperiments given a DGElist "y" from the code in toplevel question
library(csaw)
se <- SummarizedExperiment(assays ...
written 3 months ago by
ATpoint • 10
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