## User: Devon Ryan

Devon Ryan200
Reputation:
200
Status:
Trusted
Location:
Germany
Last seen:
3 years, 9 months ago
Joined:
6 years, 3 months ago
Email:
d*****@dpryan.com

#### Posts by Devon Ryan

<prev • 20 results • page 1 of 2 • next >
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... Period A and type 3 are always the same, so you can't use ~period+type as a model and hope for it to work (I imagine that this is the error you're getting). There are a few steps in DESeq2 where you can manually input a model matrix, so you might have luck going that route. I'm not going to give you ...
written 4.9 years ago by Devon Ryan200
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... Is condition.exon a typo when you made this post or is that what you actually used? If the latter, you just want condition:exon. ...
written 5.1 years ago by Devon Ryan200
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... Please don't cross-post on here and biostars. ...
written 5.1 years ago by Devon Ryan200
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... N.B., I forgot to CC the list originally. Hi Son, To add a bit to Richard's response, there's also the issue that conversion to FPKM/RPKM/TPM loses precision information. For example, suppose two samples in a group produce values of 1.0 and 1.2 for some gene (these can be any of the aforementioned ...
written 5.1 years ago by Devon Ryan200
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... Hi Alex, It's best to CC the package maintainer with questions such as these (I've done so on this reply). Keep in mind that it's the height of vacation season, so I wouldn't be overly surprised if it takes longer to get a reply. Best, Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Laborator ...
written 5.2 years ago by Devon Ryan200
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... Hi Preethy, You likely want: design=model.matrix(~pair+Treat:Phenotype, data=pdata) If that still yields the error, then you'll need to share "pdata" or "design". Also, please don't crosspost on both this list and biostars ( https://www.biostars.org/p/98907/), it duplicates the community effort. ...
written 5.5 years ago by Devon Ryan200
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... Just swap the strand in your GRanges object and then use ignore.strand=FALSE with summarizeOverlaps. Something like: strand(gr) <- ifelse(strand(gr)=="+", "-", "+") That will work unless you have features without strands, at least. Devon ____________________________________________ Devon Ryan ...
written 5.5 years ago by Devon Ryan200
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... The difference in output when running cpm() on a matrix and a DGEList is due to the latter using the normalized library size. In other words, the latter method does: t(t(currentDiff$counts)/(1e-6*currentDiff$samples$lib.size*currentDiff$samples$norm.factors)) rather than t(t(currentDiff$counts)/ ...
written 5.6 years ago by Devon Ryan200
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... Hi Antonio, I counted 13 exonic bins by eye. What do you find to be amiss there? Remember that you're not using a flattened/union gene model with DEXseq, but rather pretty much the exact opposite (maybe it should be called a "disjoint gene model"?). BTW, that first bin is actually 2bp wide. Regar ...
written 5.7 years ago by Devon Ryan200
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... Hi Veronica, The SAM file optionally output by htseq-count is mostly for debugging. You need, instead, to load the counts that are printed to the screen. If your original command was something of the form: samtools view alignments.bam | htseq-count -o alignment.htseq.sam - something.gff then simp ...
written 5.7 years ago by Devon Ryan200

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