User: Devon Ryan

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Devon Ryan200
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Germany
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d*****@dpryan.com

Posts by Devon Ryan

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Answer: A: how to design the formular
... 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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Comment: C: DEXSeq DEXSeqDataSetFromHTSeq object creation error
... 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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Comment: C: Error with goProfiles and goTools: "object org.XX.egGO not found"
... Please don't cross-post on here and biostars. ...
written 5.1 years ago by Devon Ryan200
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Answer: A: RNA-seq differentially expressed gene finding methods
... 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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Answer: A: DEXSeq continous variable in model
... 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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Answer: A: edgeR - paired samples with multifactorial design - errors
... 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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Answer: A: Rsamtools - summarizeOverlaps - count read on complementary strand
... 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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Answer: A: extracting CPM from a DGElist after normalization in edgeR
... 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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Comment: C: DEXSeq - too many exons in gene
... 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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Comment: C: Error Using DESeq with HTSeq-Count
... 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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