User: ATpoint

gravatar for ATpoint
ATpoint10
Reputation:
10
Status:
New User
Location:
Germany
Website:
https://www.biostars.o...
Last seen:
1 day, 10 hours ago
Joined:
2 years ago
Email:
a*********@gmail.com

Wet-lab biologist by training, wannaba computational biologist.

Biostars Mod: ATpoint

Posts by ATpoint

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Problem in featureCounts file.
... Cross-posted: https://www.biostars.org/p/392402/ ...
written 21 days ago by ATpoint10
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Comment: C: Paired samples in cell lines using deseq2
... 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 ATpoint10
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Comment: C: Creating contrasts which do not include the reference level in limma, edgeR or D
... 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 ATpoint10
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Comment: C: Anbiguous instruction on how to set the blind value in DESeq2's vst function
... 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 ATpoint10
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InTAD: Sample Size and Statistical Power
... 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- ...
intad written 7 weeks ago by ATpoint10 • updated 7 weeks ago by Konstantin Okonechnikov20
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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 12 weeks ago by ATpoint10
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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 ATpoint10
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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 3 months ago by ATpoint10
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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 3 months ago by ATpoint10
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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 3 months ago by ATpoint10

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