User: Stephen Henderson

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Posts by Stephen Henderson

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recount not available
... Hi I have the latest R version this morning (R3.3.3) and according to the listed BioC dependencies I believe I should be able to install the 'recount' package (NB I tried installing with R3.3.0 and updated after that didn't work). Depends R (>= 3.3.0), SummarizedExperiment Ho ...
recount written 9 weeks ago by Stephen Henderson1.0k • updated 9 weeks ago by Martin Morgan ♦♦ 20k
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Comment: C: matchPattern vmatchPattern vectorised
... matchPDict! Fantastic. That's exactly it. Sorry I missed that. Many thanks. Stephen On Dec 14, 2013 8:10 PM, =?ISO-8859-1?Q?Herv=E9_Pag=E8s?= wrote: Hi Stephen, On 12/14/2013 08:05 AM, Henderson, Stephen wrote: > thx Steve > > I hadn't heard of gmapR (and GSNAP) I will check it now. The ...
written 3.5 years ago by Stephen Henderson1.0k
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Comment: C: matchPattern vmatchPattern vectorised
... thx Steve I hadn't heard of gmapR (and GSNAP) I will check it now. The Rsubread package is a possible as I have it installed and planned to use it later in the pipeline so there is little extra overhead -- in my case. However a quick look at the documentation and code (of both) suggests that they ...
written 3.5 years ago by Stephen Henderson1.0k
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Answer: A: matchPattern vmatchPattern vectorised
... Sorry The second I sent my initial post I realised I should have said Biostrings package for the vmatchPattern function. Not BSgenome (which is the subject). Fortunately for me you seem to maintain both. So apologies for any confusion. Stephen ________________________________________ From: St ...
written 3.5 years ago by Stephen Henderson1.0k
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Answer: A: Graph for microarray data
... heatmap(matr,col=c('green','black','red'), scale='none') On 19 Sep 2008, at 13:24, Tim Smith wrote: > r1 <- matrix(0:1,11,5) > r2 <- matrix(-1:0,13,5) > matr <- rbind(r1,r2) > rownames(matr) <- LETTERS[1:nrow(matr)] > colnames(matr) <- 1:5 > heatmap(matr,col=c( ...
written 8.8 years ago by Stephen Henderson1.0k
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Answer: A: How to plot Gene Ontology categories
... Hi The datasets here are from the MSigDB (C5: Gene Ontology GeneSets) http://www.broad.mit.edu/gsea/msigdb/index.jsp Software from the same site GSEA will do a similar analysis and give not a Z-value but what they call a 'normalised enrichment score' and an FDR cutoff for significant enrichments. ...
written 9.1 years ago by Stephen Henderson1.0k
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Answer: A: analysis of 70 groups for differential expression
... I can't help feeling that running 55 contrasts is 'dredging' your data. Why not run 11 contrasts each group against everything else? Stephen Henderson Wolfson Institute for Biomedical Research Cruciform Buildging, Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 ...
written 9.8 years ago by Stephen Henderson1.0k
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Answer: A: analysis of 70 groups for differential expression
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070912/ c739a81b/attachment.pl ...
written 9.8 years ago by Stephen Henderson1.0k
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Answer: A: SAM algorithm S0 value calculation
... In the original paper: "Significance analysis of microarrays applied to the ionizing radiation response". PNAS 2001 98: 5116-5121, (Apr 24). The calculation of s0 is described thus (page 2, first column): "The coefficient of variance of d(i) was computed as a function of s(i) in moving windows acro ...
written 10.0 years ago by Stephen Henderson1.0k
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Answer: A: Affymetrix Human Exon Array MPS and PS files contain different probeset groups
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070626/ 844ebc8b/attachment.pl ...
written 10.0 years ago by Stephen Henderson1.0k

Latest awards to Stephen Henderson

Popular Question 9 weeks ago, created a question with more than 1,000 views. For heatmap colours
Centurion 3.5 years ago, created 100 posts.

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