User: David Iles

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David Iles130
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Posts by David Iles

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Answer: A: BiSeq - readBismark error
... Hi, Thanks for the warning. When will the BiSeq 1.2.4 package be available? I?m about to start a methylation analysis ?. Dr David Iles Visiting Research Fellow School of Biology University of Leeds Leeds LS2 9JT UK d.e.iles at leeds.ac.uk On 5 Feb 2014, at 17:29, Hans-Ulrich Klein > wrote ...
written 5.8 years ago by David Iles130
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Comment: C: locate a target species in Refseq ftp directory
... Hi Heyi, You could try the following link to the sheep sequencing consortium web site. You'll find links to gff files there with known and predicted mRNAs, together with the latest draft assembly of the sheep genome sequence (together with thousands of unmapped scaffolds and contigs .....) http:// ...
written 6.1 years ago by David Iles130
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Comment: C: parallel and GSVA
... Hi Robert, You appear to be correct in your assumption that there may be an issue with the GSVA package running in the R64.app GUI on a Mac. Following Steve's suggestion, the following went smoothly running R from Terminal: > leukemia_es <- gsva(leukemia_filtered_eset, c2BroadSets,min.sz=10, ...
written 6.9 years ago by David Iles130
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Comment: C: parallel and GSVA
... Hi Robert, Thanks for your prompt response. Yes, setting parallel.sz=1 does work. Thanks for that. I have 8 cores available, so can I set parallel.sz=8? Thanks Dave Dr David Iles School of Biology University of Leeds Leeds LS2 9JT d.e.iles at leeds.ac.uk On 11 Jan 2013, at 13:11, Robert C ...
written 6.9 years ago by David Iles130
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parallel and GSVA
... Hi Folks, I want to run a GSVA analysis on a set of Affymetrix hgu133plus2 arrays. To familiarise myself with the GSVA code, I worked through the example in the vignette, but encountered the following issue... > data(leukemia) > data(c2BroadSets) > library(parallel) > filtered_eset < ...
process gsva written 6.9 years ago by David Iles130 • updated 6.9 years ago by Steve Lianoglou12k
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vmatchPDict?
... Hi, I need to re-map the probe sequences of the Affymetrix Bovine genome array to a recent draft sequence of the sheep genome (please, don't ask why...). As a first step, I successfully created a new BSgenome package from a seed file, listing individual chromosomes as 'seqnames' and unmapped, and t ...
bsgenome probe written 6.9 years ago by David Iles130 • updated 6.9 years ago by Hervé Pagès ♦♦ 14k
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Comment: C: Problems installing sva and bladderbatch
... Hi, I have experienced similar issues with a number of R packages (not all from BioC - e.g. Rwave; see below) since upgrading to R 2.14 last week. A solution would be much appreciated - I'm in the middle of a wavelet analysis! Dr David Iles Institute for Integrative and Comparative Biology Univer ...
written 8.0 years ago by David Iles130
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Comment: C: unable to install qvalue..
... Hi Simon, I have recently installed tcltk manually into R - you can then get R to use tcltk automatically from wherever the software is installed. Download the latest tcltk tar.gz file from sourceforge (check out http://sourceforge.net/projects/tcl/files/Tcl/) and unpack it, eg into the R library ...
written 8.7 years ago by David Iles130
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Comment: C: unable to install qvalue..
... Hi Simon, Check out this URL. http://www.tcl.tk/software/tcltk/ Various tcltk widgets are also available from http://sourceforge.net/. Use the search engine to locate tools such as BWidget, tcllib, tcltable etcetc. Dave Dr David Iles Institute for Integrative and Comparative Biology University ...
written 8.7 years ago by David Iles130
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Comment: C: what's really in hgu133plus2.db?
... Jim, Thanks for your response. The point of understanding exactly where a probeset is located is of fundamental importance because it is now clear from the ENCODE project that around 90% of genome sequence is actively transcribed in a regulated way - John Mattick presented an excellent talk introdu ...
written 8.8 years ago by David Iles130

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Popular Question 4.8 years ago, created a question with more than 1,000 views. For what's really in hgu133plus2.db?

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