User: rbronste

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rbronste60
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Posts by rbronste

<prev • 113 results • page 1 of 12 • next >
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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 9 weeks 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 9 weeks ago by rbronste60
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Comment: C: DESeq2 design and stats question
... Thanks again! ...
written 11 weeks 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 11 weeks 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 11 weeks 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 12 weeks ago by rbronste60 • updated 11 weeks ago by Michael Love17k
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Comment: C: biomaRT biotype TFs only
... I guess filtering one list vs the other for  "external_gene_name" ...
written 12 weeks 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 12 weeks ago by rbronste60
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biomaRT biotype TFs only
... Hi I am trying to retrieve from biomaRT a GRanges of only TFs with their gene identifier metadata and was not sure about how to do this, I assume its looking through the particular biotype but not sure if this applies to gene or specific transcripts? Thank you! ...
mus musculus biomart ensembl tf biotype written 12 weeks ago by rbronste60 • updated 12 weeks ago by Mike Smith2.6k
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Error in DESeq2 plotMA from object subset
... I am having a bit of trouble getting an MAplot from a result subset (though ?plotMA says this is possible) of a DESeq2 dataset. I am doing the following and getting this error: > plotMA(BN_group_female_padj.01, alpha = .01, contrast=c("group", "femaleBB", "femalevehicle") ,ylim=c(-10,10)) Error ...
deseq2 subset maplot written 12 weeks ago by rbronste60 • updated 12 weeks ago by Michael Love17k

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