User: ATpoint
ATpoint • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Germany
- Website:
- https://www.biostars.o...
- Last seen:
- 1 week, 3 days ago
- Joined:
- 1 year, 10 months ago
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Wet-lab biologist by training, wannaba computational biologist.
Biostars Mod: ATpoint
Posts by ATpoint
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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 4 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 5 weeks 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 6 weeks 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 6 weeks 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 6 weeks ago by
ATpoint • 10
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... This I understand but how about obtaining normalized counts for non-GLM applications like clustering or checking normalization efficiency by MA plots. Can you use the offsets for those, too? ...
written 6 weeks ago by
ATpoint • 10
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... I imported a set of `salmon` quantifications into R with `tximport` default settings and exactly used the code on the manual page for [tximport][1] to prepare data for use with `edgeR`. The result is a `DGElist` with the offsets for the downstream DGE analysis.
Issue: The `DGElist` (`y$samples`) do ...
written 6 weeks ago by
ATpoint • 10
• updated
6 weeks ago by
James W. MacDonald ♦ 50k
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... Dear Michael,
I think there is a little flaw in the source code of `lfcShrink` with DESe2 version 1.22.2. Given one wants to turn off the `svalue` calculation one would set `svalue=F`. Still in the code if one sets type="apeglm" the svalue will in any case be turned on without respecting the value ...
written 10 weeks ago by
ATpoint • 10
• updated
10 weeks ago by
Michael Love ♦ 24k
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... Thank you. Just out of interest, because I encountered this problem also on a different and unrelated dataset with larger sample sizes, suggesting that this is a rather general issue when n becomes large. Do you plan to make changes in future versions of `apeglm` to compensate for this issue interna ...
written 5 months ago by
ATpoint • 10
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... You should at least provide the MA plot and some data to reproduce what you've stated in the question. The DESeq2 object saved in a rdata file would be an option.
...
written 8 months ago by
ATpoint • 10
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