User: Chris Stubben

gravatar for Chris Stubben
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Salt Lake City, Utah
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2 days, 2 hours ago
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1 year, 8 months ago
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Posts by Chris Stubben

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Gviz color alignments by read strand
... This only works if ALL reads are plotted in the display. ...
written 6 weeks ago by Chris Stubben40
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Answer: A: Gviz color alignments by read strand
... I can color by read strand if I subset a data.frame before creating the alignments track.   bam1 <- readGAlignments(BamFile(system.file(package="Gviz", "extdata", "gapped.bam"))) bamdf <- data.frame(bam1) names(bamdf)[1] <- "chromosome" bamdf <- subset(bamdf, start > 2997000 & e ...
written 6 weeks ago by Chris Stubben40
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Gviz color alignments by read strand
... Is there a way to use fill.reads to color alignments by read strand?  I would like to plot these on a single track library(Gviz) alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata",   "gapped.bam"), isPaired=FALSE) plotTracks(alTrack, from=2997000, to=2998200, chromosome="chr12", ...
gviz written 7 weeks ago by Chris Stubben40
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Comment: C: compare one group to mean of two others in DESeq2 with betaprior=FALSE
... Is there any way to shrink fold changes if you use  ~0 + trt?  With betaPrior = FALSE, I get the same error at a later step running lfcShrink(dds, contrast= c("trt", "C", "A")) ...
written 9 months ago by Chris Stubben40
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Comment: C: compare one group to mean of two others in DESeq2 with betaprior=FALSE
... Thanks, I remember reading that you should not use ~0 + trt, but that must be when betaPrior=TRUE ...
written 9 months ago by Chris Stubben40
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compare one group to mean of two others in DESeq2 with betaprior=FALSE
... Is it possible to compare one group with the mean of two others if betaPrior=FALSE?   In previous versions of DESeq2, I could group C vs A+B using a list below, but I'm not sure how to work with the new resultsNames output like trt_B_vs_A. dds <- makeExampleDESeqDataSet(n=1000, m=18) dds$trt &l ...
deseq2 written 9 months ago by Chris Stubben40 • updated 9 months ago by Michael Love20k
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Scan error using biomart with version option
... I get a scan error if I use the version option in biomaRt while running latest R version 3.4.2.    ensembl <- useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl", version=90) ensembl@host [1] "http://e90.ensembl.org:80/biomart/martservice" getBM(attributes=c('ensembl_gene_id','externa ...
biomart written 11 months ago by Chris Stubben40 • updated 10 months ago by Mike Smith3.1k
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Comment: C: Reordering factor levels in DESeq2 causes results error in cleanContrast
... It's not very clear in the Note on Factor Levels in the DESeq2 vignette that you should not reorder factors after running DESeq2.   I will only reorder factors in sample tables from now on. ...
written 12 months ago by Chris Stubben40
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Reordering factor levels in DESeq2 causes results error in cleanContrast
... I recently updated to R version 3.4.2 and noticed that DESeq2 results now returns an error if I relevel the factors.   library(DESeq2) cnts <- matrix(rnbinom(n=1000, mu=100, size=1/0.5), ncol=10) samp <- data.frame( cond=factor(rep(c("a", "b"), each=5))) dds <- DESeqDataSetFromMatrix(cnts ...
deseq2 written 12 months ago by Chris Stubben40 • updated 12 months ago by Michael Love20k

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Popular Question 7 months ago, created a question with more than 1,000 views. For Scan error using biomart with version option
Student 7 months ago, asked a question with at least 3 up-votes. For Scan error using biomart with version option

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