James, There is an annotation package, just not a release version (which is why you don't see it on on the BioC website). You can use install.packages2("mouse4302", develOK=TRUE) to get it. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> James Wettenhall <wettenhall@wehi.edu.au> 08/22/04 9:24 AM >>> Hi, I know this has been discussed before: https://stat.ethz.ch/pipermail/bioconductor/2003-July/002025.html but is anyone working on a Bioconductor-style annotation package for the Affy mouse chip 430_2 ? I've downloaded the annotation from the Affy website in a CSV (comma-separated values) file, but it would be nice to have it in a standard Bioconductor format (an R package), especially for affylmGUI. I hoping to avoid coding complicated dialogs in affylmGUI to allow imported arbtirary annotation files, but I'd be happy to hear opinions on whether it would be good to have a simple mechanism to import some CSV annotation files into affylmGUI somehow. I've had a quick look at AnnBuilder, but this seems to be more for adding extra annotation columns from the web, whereas I have plenty of annotation columns already in the CSV file (enough for our purposes). I just want to get them in a standard BioC format. I tried just manually creating an annotation package, but when I tried saving one of the required .rda (RData) files in the data/ directory of the package (e.g. for gene symbols), I found that I then could not load the saved .rda file into R - I got the error Error: protect(): stack overflow I've tried it on my laptop (1GB memory) and on a Linux machine with a lot more memory. So if anyone has an annotation package for this chip that would be great. Or if anyone can steer me in the right direction as far as making an annotation package from the CSV file that would be great. Or if anyone wants to share some R code for reading data from Affy CSV files that would be great too. Regards James _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

On Sun, 22 Aug 2004, James MacDonald wrote: > There is an annotation package, just not a release version (which is why > you don't see it on on the BioC website). You can use > install.packages2("mouse4302", develOK=TRUE) to get it. Hi Jim, Thanks for that. Got it! Thanks Jianhua for building the package. Regards, James