User: rbronste

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rbronste50
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@RBronshteyn
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Posts by rbronste

<prev • 103 results • page 2 of 11 • next >
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Matrix not full rank - DESeq2
... Hi, Trying to do the following and getting an error of Model matrix not full rank: sampleNames<-c("MMV1", "MMV2", "MMV3", "FMV1", "FMV2", "FMV3", "MME7", "MME8", "MME9", "FME1", "FME2", "FME3") sampleSex<-c("male", "male", "male", "female", "female", "female", "male", "male", ...
deseq deseq2 model.matrix differential binding analysis model matrix not full rank written 3 days ago by rbronste50 • updated 2 days ago by Simon Anders3.4k
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Comment: C: Intergenic coordinates with Genomic Feaures
... Its interesting but I tried both methods and it worked to get these regions, then I did the following: intersect_intergenic<-intersect(intergenicRegions2, resMa, ignore.strand=TRUE) I intersected some data I had which I know contains intervals that overlap a small number of promoters and a la ...
written 10 days ago by rbronste50
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Filtering a BED file according to genomic annotation
... I was wondering about a straightforward way to take a GRanges for instance that originate from a BED file and pull out intervals specific to different genomic features such as promoters or intronic/intergenic ChIP-seq peaks etc? Thanks.  ...
chipseq filtering bedtools bed files written 11 days ago by rbronste50 • updated 11 days ago by Aaron Lun18k
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Comment: C: SummarizedExperiment object from GEOquery obtained GSE
... Actually one other quick question, the (filter_regex='bed'), will this also eliminate the .tar files that contain .bed files from retrieval and only get the bed.gz files listed in supp data?  ...
written 17 days ago by rbronste50
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Comment: C: SummarizedExperiment object from GEOquery obtained GSE
... Thanks, exactly what I was after! ...
written 17 days ago by rbronste50
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Comment: C: SummarizedExperiment object from GEOquery obtained GSE
... No I don't mean that it should be a single SummarizedExperiment object (sorry bad wording on my part), just that I would obtain 10 SE objects simultaneously with associated GRanges. Just in general what is the most straightforward and direct way to do this?  ...
written 17 days ago by rbronste50
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SummarizedExperiment object from GEOquery obtained GSE
... I was wondering if there was a straightforward way to take a GEOquery downloaded GSE, which I get in the following way: gse <- getGEO("GSE63137",GSEMatrix=FALSE) and to create a SummarizedExperiment object with representative ranges? If the GSE has for instance 10 bed files, is there a quick w ...
geoquery summarizedexperiment matrix geo written 19 days ago by rbronste50 • updated 17 days ago by Sean Davis21k
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Comment: C: ChIPSeeker enrichPeakOverlap external dataset downloads
... Is there any way to just retrieve the BED files and exclude the bedGraph files? ...
written 22 days ago by rbronste50
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Comment: C: ChIPSeeker enrichPeakOverlap external dataset downloads
... Great thanks! Can I currently update this commit with update.packages("ChIPseeker")? ...
written 22 days ago by rbronste50
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Comment: C: ChIPSeeker enrichPeakOverlap external dataset downloads
... So basically it downloads about 10 files and then quits on this one because I guess it can't locate it. Any way around this? ...
written 23 days ago by rbronste50

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