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Oops, "virtual integration" in the 2nd sentence of my previous post should have been "vertical integration". Gordon

I have committed to the BioC 1.8 release branch bug fixes for limma functions read.imagene() and plotMA3by2(). The release version number of limma is incremented to 2.6.2. Gordon

Before using winMenuAdd(), is it possible to test whether the menu already exists? One could use try(winMenuAddItem()) with appropriate arguments, but is there anything more elegant? Many thanks Gordon

At 03:06 PM 4/11/2005, Vincent Carey 525-2265 wrote: >the biocViews HTML documents had not been refreshed for some time. >i just refreshed them and limma is visible. Thanks :) Gordon

My previous post should have had this subject heading - my apologies. Gordon --------------------------------------------------------------------------------------- Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3050, Australia Tel: (03) 9345 2326, Fax...

I've committed limma 1.8.18 to the repository today. lmFit() is now *much* faster for a typical affy analysis, which usually doesn't involve NAs or probe-set specific weights. There were some teething problems with special cases...

PS. The line added by Sweave to a vignette in R2.4.0dev for Windows is actually \usepackage{C:/PROGRA~1/R/R-24~1.0DE/share/texmf/Sweave} Even though this DOS version of the file path doesn't...

The link to "MacOS X check summary" on the page http://cran.r-project.org/src/contrib/PACKAGES.html is broken. Gordon --------------------------------------------------------------------------------------- Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics, Walter and Eliza Hall Institute of Medical Research, 1G Royal...

I want edgeR to bump to a major new version 4.0.0 for the Bioconductor 3.17 release this month. If I set the edgeR version to 3.99.0 on the developmental repository now, will that bump to...

Many thanks to Hadley Wickham for pointing out that my question had already been answered on the R-help list in December, see https://www.stat.math.ethz.ch/pipermail/r-help/2003-December/041786.html or http://maths.newcastle...

I'd like to create a suitable batch file or shortcut so that I can run Sweave on a .Rnw or .Rtex file simply by clicking on the file from Windows Explorer in Windows XP (as I do with latex...

I was curious to read the following in the "Guidelines for Rd files" at http://developer.r-project.org/Rds.html: "For consistency, aim to use British (rather than American) spelling. (NB: British spelling often uses -ize as in `capitalize...

There has been no Windows binary for the GenomicRanges package since version 1.31.12, which was nearly 2 months ago. This means that I can't install GenomicFeatures either, because it depends on a later version of GenomicRanges, so...

Here's a Rd link which has worked for many years in the html and chm help pages, and still works fine in R 2.10.10: \link[limma:00Index]{LIMMA contents page} Despite working fine, this is now flagged...

An rbind() method or an rbind-like function for ExpressionSet objects would be useful. Any plans for such a function? At the moment, an ExpressionSet object can be subsetted by rows or columns. Column subsets can be put back together...

Dear Bioc team, The Bioc package home pages link out to a code browser, which is a very useful resource to be able to refer external users or reviewers to. The code browser seems to be down at the moment...

I have committed to the BioC 2.0 release branch some minor bug fixes to the limma package. The release version number of limma is incremented to 2.10.3. It is currently the same as limma 2.11.3...

Thanks for the reply. Apologies for checking only R patched rather than R-devel. I guess that this means that someone must have a use for allowEscapes=TRUE when read reading a file in table format into a data frame...

>Note also that R does have a User Guide, i.e., while there is plenty of >excellent documentation, >there is no single document which is a guide to the whole project. Oops, I meant to write "R does not have...

Just reporting a possible issue with the display of author ORCID IDs on Bioconductor package landing pages. On the release (Bioconductor 3.20) package landing pages, ORCID IDs are not displayed, even if they are included in the package DESCRIPTION...