User: Cornwell, Adam
Cornwell, Adam • 110
- Reputation:
- 110
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- Location:
- United States
- Last seen:
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- Joined:
- 6 years, 3 months ago
- Email:
- a************@urmc.rochester.edu
Posts by Cornwell, Adam
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... Hi, I'm trying to run IntEREst on BAM files from a single-ended experiment. It runs for a while, then I get an error:
Error in interestAnalyse(reference = reference, bamFile = bamFile, isPaired = isPaired, :
object 'resTmpPair' not found
Calls: do.call ... mapply -> -> interes ...
written 13 days ago by
Cornwell, Adam • 110
• updated
10 days ago by
ali.oghabian • 0
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... Nice, I suppose that was added since the last time I went through the limma documentation since I haven't come across it before.
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written 5 months ago by
Cornwell, Adam • 110
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... I recently looked at a section of a paper (unpublished) in which the authors, wary of introducing spurious correlations when comparing two sets of DESeq2 foldchanges, ended up computing foldchanges for two sample groups against two different subsets of their control samples. The potential issue is s ...
written 5 months ago by
Cornwell, Adam • 110
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... Hi,
I have been working on an RNA-Seq dataset on which I applied RUVSeq (ruvr method) at the gene-count level to account for some unexpected variance before running DESeq2. I am also working on using DEXSeq to look at differential exon usage. Optimally, I would be able to also apply RUVSeq to the b ...
written 2.3 years ago by
Cornwell, Adam • 110
• updated
2.2 years ago by
davide risso • 810
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... Thanks for the info!
...
written 3.4 years ago by
Cornwell, Adam • 110
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... I'm trying the model you suggested, which got through testForDEU, but I'm further not sure what to do for calculating fold changes with estimateExonFoldChanges. DESeq2 allows fetching results for anything that comes up in resultsNames(). However, DEXSeq seems to only allow fetching foldchanges for c ...
written 3.4 years ago by
Cornwell, Adam • 110
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... Just to confirm- I am looking for differential exon usage attributable to differences in the treatment across the strains- I don't need the triple interaction term to get that?
This is the first time I've had to do this full model/reduced model specification, and it's a little confusing.
...
written 3.4 years ago by
Cornwell, Adam • 110
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... I am trying to run DEXSeq and running into an issue where I get an error when I try to run testForDEU:
unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
After running through testForDEU with the debugger, I noticed the following issue with degrees of freedom, which ...
written 3.4 years ago by
Cornwell, Adam • 110
• updated
3.4 years ago by
Alejandro Reyes • 1.6k
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... Greetings,
I started working with RUVnormalize a couple of days ago, and although I wasn't able to get the iterative method to work (due to an external package that is very difficult to get working on Windows) the naive methods seemed to at least do something. However, the vignette does not spec ...
written 3.9 years ago by
Cornwell, Adam • 110
• updated
3.8 years ago by
laurent.jacob • 10
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... Thank you for the clarification. I didn't come across anything to
indicate that the bimap interfaces were effectively deprecated. Is
there a page or post or something that has current best practices for
working with annotation? Many vignettes and example workflows still
include methods other than se ...
written 4.9 years ago by
Cornwell, Adam • 110
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