User: rbronste

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rbronste60
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@RBronshteyn
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Posts by rbronste

<prev • 125 results • page 2 of 13 • next >
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3x2 comparisons in DEseq - time (3 time points) and two treatments
... Currently just using the following setup to look at differences in treatment across all 3 time points I have (30, 180, 360 min) however would like to also break down analysis by time, any suggestions for design would be much appreciated thank you! hyMData<-read.csv("hyM.csv") rownames(hyMData) ...
deseq deseq2 rna-seq multiple comparisons written 3 months ago by rbronste60 • updated 3 months ago by Michael Love19k
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Most liked/utilized qPCR analysis package
... Wondering about the current state of thought on this? Does not have to be a high throughput, just something straightforward to use and uses data from StepOne Plus qPCR machine. Thanks! ...
qpcr written 5 months ago by rbronste60 • updated 5 months ago by Gordon Smyth35k
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Comment: C: DESeq2 design subcategories
... Thanks for the tip! The code in the vignette refers to doing this with raw counts and I was more interested in doing this with output of results() such as from: results(dds, contrast=c(1, -1/3, -1/3, -1/3)) With all four possible coefficients plotted. Thanks again! ...
written 8 months ago by rbronste60
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Comment: C: DESeq2 design subcategories
... A bit of a tangential question, but do you have any suggestions on how to effectively visualize results of something like this comparison, basically some kind of 4-way (dimension) graph that shows differential peaks unique to each of the 4 categories? Thanks! ...
written 8 months ago by rbronste60
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Comment: C: DESeq2 design and stats question
... Thanks again! ...
written 8 months ago by rbronste60
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Comment: C: DESeq2 design and stats question
... Ok great thanks will put in that additional comparison, but in terms of the actual contrast I guess it would be the following, for male vs female only: contrast=c(1/2, -1/3, -1/2, -1/3) I guess just a little confused in this format for how to specify the comparison, not as much in the vignette.  ...
written 8 months ago by rbronste60
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Comment: C: DESeq2 design and stats question
... Thanks!  My central question here is whether the design makes sense for the two ways in which I am retrieving results?  Also, in addition, I was noticing that when I lfcThreshold the #1 result type (a comparison of the BB vs vehicle in males) at the same cutoff as #2 I get pretty much no diff peak ...
written 8 months ago by rbronste60
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DESeq2 design and stats question
... So will just list current design first and then get into the question: rangedCounts <- dba.peakset(Adult_BN_count, bRetrieve=TRUE) nrows <- 1054182 ncols <- 12 counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows) rowRanges<-GRanges(rangedCounts) sampleNames<-c("MBV1", "MB ...
deseq deseq2 differential binding analysis atac-seq written 8 months ago by rbronste60 • updated 8 months ago by Michael Love19k
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Comment: C: biomaRT biotype TFs only
... I guess filtering one list vs the other for  "external_gene_name" ...
written 8 months ago by rbronste60
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Comment: C: biomaRT biotype TFs only
... Very helpful thank you!  My aim here is to filter a full HT-seq list of counts for factors with DNA binding activity and do it in such a way as to grab only those above some cutoff, lets say just DNA binding factors with absolute counts above 100 for example. Do you think just importing that list a ...
written 8 months ago by rbronste60

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Centurion 16 months ago, created 100 posts.
Supporter 16 months ago, voted at least 25 times.

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