User: rbronste

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rbronste20
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Posts by rbronste

<prev • 64 results • page 2 of 7 • next >
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Comment: C: Altering design following DESeqDataSetFromMatrix and DESeq
... Any thoughts on this final question? Thanks so much!  ...
written 3 days ago by rbronste20
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Comment: C: Altering design following DESeqDataSetFromMatrix and DESeq
... Sorry pasted the wrong line. I def am not interested in the high p-value result for export, was moreso trying to a quick way to export for instance sites that are differential within sex (under some low cutoff, with treatment remaining steady) or conversely within treatment. I did not see a clear de ...
written 9 days ago by rbronste20
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Comment: C: Altering design following DESeqDataSetFromMatrix and DESeq
... Thanks for explanation Michael.  I can see now that looking via the following will give me what I need: plotCounts(dds, gene=which.min(res$padj), intgroup = "sex") plotCounts(dds, gene=which.max(res$padj), intgroup = "sex") At least on a site by site basis. What is an easy way to export such re ...
written 9 days ago by rbronste20
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Altering design following DESeqDataSetFromMatrix and DESeq
... I was wondering if it was possible to augment design, flip lets say: dds<-DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ treatment + sex)​ to dds<-DESeqDataSetFromMatrix(countData = countData, ...
deseq2 differential binding analysis written 9 days ago by rbronste20 • updated 9 days ago by Michael Love14k
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Unable to find an inherited method for function distanceToNearest for signature GRanges
... Attempting to run chipenrich on sample data set: chipenrich(peaks = peaks_E2F4, genome = 'hg19', genesets = c('GOBP', 'GOCC', 'GOMF'), locusdef = "nearest_tss", qc_plots = FALSE, out_name = NULL, n_cores = 1)​ Running into the following error after some processing: Reading peaks from data.frame ...
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Comment: C: Structure of DiffBind dba.count matrix equivalent to DESeqDataSetFromMatrix inpu
... Thanks for the info Rory! Thats pretty much what I have been doing. Is there a good way on the back end, once I do whatever interaction analysis with DESeq2, to quickly interrogate specific intervals (differential/interacting ones I find interesting) when the site interval ranges are removed from th ...
written 12 days ago by rbronste20
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Structure of DiffBind dba.count matrix equivalent to DESeqDataSetFromMatrix input?
... Wondering if the basic matrix output from dba.count in DiffBind would be an appropriate input matrix into DESeq2 (via DESeqDataSetFromMatrix) or if has to be modified in some other fashion? I want to run DESeq2 interactions on this interval read count matrix generated by DiffBind. Thank you. ...
diffbind deseq2 written 15 days ago by rbronste20 • updated 14 days ago by Rory Stark2.1k
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Comment: C: Interaction with DESeq2 via DiffBind
... Thanks Rory! Would it be fair to use the dba.count output matrix and feed that into DESeq2 via DEseqDataSetFromMatrix? So as to get around having to manually create a read depth adjusted matrix for all of your peaks? Thanks again. ...
written 17 days ago by rbronste20
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Comment: C: Pre-filtering DESeqDataSetFromMatrix input
... Thank you! Stupid mistake on my part for sure... ...
written 19 days ago by rbronste20
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Pre-filtering DESeqDataSetFromMatrix input
... A little confused about this, wanted too filter out lines in the matrix with read counts lower than 10 to speed up DESeq2 processing using the following: dds <- dds[ rowSums(counts(dds)) > 10, ] However just as before the filtering, after the filtering countData looks like this: head(coun ...
deseq2 differential binding analysis written 19 days ago by rbronste20 • updated 19 days ago by James W. MacDonald45k

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