[BioC] Affy Mouse 430_2 annotation

[James MacDonald]

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 at 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 at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor