User: Jessica Perry Hekman

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Posts by Jessica Perry Hekman

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Comment: C: Expected number of DE genes?
... Thanks, Simon. I did expect a fair amount of noise, and I think a lot of my surprise came from the fact that I expected the noise to be expressed as a large number of positives. Your explanation helps adjust my perspective. Jessica On 07/16/2014 01:12 AM, Simon Anders wrote: > Dear Jessica > ...
written 3.4 years ago by Jessica Perry Hekman140
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Comment: C: Expected number of DE genes?
... Thanks, Tom. Yes, you summarized my dilemma well, although I am more concerned with false negatives right now than false positives (as we do intend to do PCR to validate any positives we get, but any false negatives lost are lost forever :). Ryan also suggested PCA and I'll definitely be trying tha ...
written 3.4 years ago by Jessica Perry Hekman140
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Comment: C: Expected number of DE genes?
... On 07/15/2014 05:32 PM, Steve Lianoglou wrote: > We can only help you to answer the last point, but to do so we will > need to see the code you used and an explanation of your dataset (ie. > which samples are which condition). > > Also: why do you expect to get upwards of a thousand ...
written 3.4 years ago by Jessica Perry Hekman140
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Comment: C: Expected number of DE genes?
... Ryan -- that's extremely helpful, thanks! I'll try PCA and look at my dispersion estimates and see what light that sheds. Much appreciated. Jessica Jessica P. Hekman, DVM, MS PhD student, University of Illinois, Urbana-Champaign Animal Sciences / Genetics, Genomics, and Bioinformatics On 07/15/2 ...
written 3.4 years ago by Jessica Perry Hekman140
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Expected number of DE genes?
... I'm getting only a few dozen differentially expressed genes when I analyze my RNA-Seq data with DESeq2 (79) and EdgeR (34) (even fewer when I use EBSeq). I had expected many more -- hundreds or even a thousand. If this is the real answer, I'm fine with it, but I'm concerned that I'm doing something ...
genetics edger deseq2 written 3.4 years ago by Jessica Perry Hekman140 • updated 3.4 years ago by Thomas Hampton740
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Comment: C: Problem running summarizeOverlaps()
... On 05/22/2014 10:10 AM, Martin Morgan wrote: >> gnCnt <- GenomicAlignments::summarizeOverlaps(exByGn, bamfls, >> mode="Union", >> ignore.strand=TRUE, single.end=TRUE, param=param) >> >> OUTPUT: >> >> Error in array(x, c(length(x), 1L), if (!is.n ...
written 3.5 years ago by Jessica Perry Hekman140
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Comment: C: Problem running summarizeOverlaps()
... On 05/20/2014 04:25 PM, Martin Morgan wrote: > If you do decide to update your R, summarizeOverlaps has moved to > GenomicAlignments. So I figured if I was going to be having this much trouble I might as well be on the latest R in case that helped. So I upgraded to 3.1.0 and the latest Bioco ...
written 3.5 years ago by Jessica Perry Hekman140
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Comment: C: Problem running summarizeOverlaps()
... I used bamfls <- BamFileList(fls, yieldSize=100000) options(mc.cores=8) somewhat arbitrarily. With these settings, on my server, summarizeOverlaps() takes less than ten minutes to run, so it seems efficient enough for my purposes, but I'd be curious to hear Martin's response to Ryan's question. ...
written 3.5 years ago by Jessica Perry Hekman140
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Comment: C: Problem running summarizeOverlaps()
... On 05/20/2014 02:20 PM, Jessica Perry Hekman wrote: >>> Error: C stack usage is too close to the limit >> You might then try adding a 'yieldSize' argument to the following line, >> starting small (e.g., 100000) and moving toward the default (1000000) if >> the small size ...
written 3.5 years ago by Jessica Perry Hekman140
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Comment: C: Problem running summarizeOverlaps()
... On 05/20/2014 11:05 AM, Martin Morgan wrote: >> Error: C stack usage is too close to the limit >> > I haven't seen this error before in the context of summarizeOverlaps, so > it's a bit puzzling. I'd first check that the > > fls <- list.files("../../bam/", pattern="fo ...
written 3.5 years ago by Jessica Perry Hekman140

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Popular Question 3.4 years ago, created a question with more than 1,000 views. For Problem running summarizeOverlaps()

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