User: ATpoint

gravatar for ATpoint
ATpoint20
Reputation:
20
Status:
New User
Location:
Germany
Website:
https://www.biostars.o...
Last seen:
33 minutes ago
Joined:
2 years, 1 month ago
Email:
a*********@gmail.com

Wet-lab biologist by training, wannaba computational biologist.

Biostars Mod: ATpoint

Posts by ATpoint

<prev • 26 results • page 2 of 3 • next >
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Comment: C: DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' lengt
... 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 3 months ago by ATpoint20
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Comment: C: Correct use of tximport in combination with edgeR cpm()
... 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 ATpoint20
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Comment: C: Correct use of tximport in combination with edgeR cpm()
... 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 4 months ago by ATpoint20
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Comment: C: scATAC-seq analysis, data preprocessing
... Cross-posted on [Biostars][1] as suggested by Aaron. [1]: https://www.biostars.org/p/379520/ ...
written 4 months ago by ATpoint20
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Comment: C: Correct use of tximport in combination with edgeR cpm()
... 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 4 months ago by ATpoint20
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Comment: C: Correct use of tximport in combination with edgeR cpm()
... 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 4 months ago by ATpoint20
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Correct use of tximport in combination with edgeR cpm()
... 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 ...
edger tximport written 4 months ago by ATpoint20 • updated 4 months ago by James W. MacDonald51k
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Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
... 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 ...
deseq2 apeglm written 5 months ago by ATpoint20 • updated 5 months ago by Michael Love25k
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Comment: C: Unexpected MAplot after apeglm shrinkage in DESeq2
... 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 7 months ago by ATpoint20
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Comment: C: DESeq2 MA plot normalisation Issue
... 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 10 months ago by ATpoint20

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