User: Cornwell, Adam

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Posts by Cornwell, Adam

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Are spurious correlations possible in correlating two DESeq2 foldchanges compute
... Nice, I suppose that was added since the last time I went through the limma documentation since I haven't come across it before. ...
written 25 days ago by Cornwell, Adam110
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Are spurious correlations possible in correlating two DESeq2 foldchanges computed using the same reference sample group?
... I recently looked at a section of a paper (unpublished) in which the authors, wary of introducing spurious correlations when comparing two sets of DESeq2 foldchanges, ended up computing foldchanges for two sample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 ...
deseq2 correlation written 27 days ago by Cornwell, Adam110
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Appropriate to apply RUVSeq to exon bin counts for DEXSeq?
... 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 ...
rnaseq dexseq ruvseq written 23 months ago by Cornwell, Adam110 • updated 22 months ago by davide risso780
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Comment: C: Translating model formula from DESeq to DEXSeq
... Thanks for the info! ...
written 3.1 years ago by Cornwell, Adam110
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Comment: C: Translating model formula from DESeq to DEXSeq
... 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 3.1 years ago by Cornwell, Adam110
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Comment: C: Translating model formula from DESeq to DEXSeq
... 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 3.1 years ago by Cornwell, Adam110
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Translating model formula from DESeq to DEXSeq
... 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 ...
dexseq linear model formula written 3.1 years ago by Cornwell, Adam110 • updated 3.1 years ago by Alejandro Reyes1.6k
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RUVnormalize- should input be pre-normalized?
... 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 ...
microarray normalization ruvnormalize written 3.5 years ago by Cornwell, Adam110 • updated 3.4 years ago by laurent.jacob10
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Comment: C: Transcript clusters missing from hugene20sttranscriptcluster.db
... 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 4.5 years ago by Cornwell, Adam110
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Transcript clusters missing from hugene20sttranscriptcluster.db
... Hello, I've been working with hugene20sttranscriptcluster.db_2.14.0 (most recent release version) for the last couple of days, and noticed that some of our usual marker genes appear to not be present in the annotation package. These genes are present in current and previous versions of the Affymetr ...
annotation probe written 4.5 years ago by Cornwell, Adam110 • updated 4.5 years ago by James W. MacDonald48k

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