User: Chris Stubben

gravatar for Chris Stubben
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Salt Lake City, Utah
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1 day, 2 hours ago
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11 months, 3 weeks ago
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Posts by Chris Stubben

<prev • 6 results • page 1 of 1 • next >
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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 16 days ago by Chris Stubben10
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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 16 days ago by Chris Stubben10
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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 16 days ago by Chris Stubben10 • updated 16 days ago by Michael Love16k
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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 8 weeks ago by Chris Stubben10 • updated 5 weeks ago by Mike Smith2.5k
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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 3 months ago by Chris Stubben10
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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 3 months ago by Chris Stubben10 • updated 3 months ago by Michael Love16k

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