Hi Although I can find the rae230a and rae230b rat annotation metadata packages on the Bioconductor site, there doesn't seem to be one for the rat 230 2.0 chip (which is the combination of rae230a and rae230b). Is one available anywhere, and if not what would be the easiest way to make one (e.g. is is feasible to merge the two existing packages)? Many thanks David Prof David Kipling Department of Pathology School of Medicine Cardiff University Heath Park Cardiff CF14 4XN Tel: 029 2074 4847 Email: KiplingD@cardiff.ac.uk

Hi, Annotation for this array is available also via the biomaRt package. The array is known there as rat230_2. You can use as follows: > mart<-martConnect() > getGene(id="1387055_at", array="rat230_2",mart=mart) Slot "id": [1] "1387055_at" Slot "table": $symbol [1] "APBP1_RAT" $description [1] "Amyloid protein-binding protein 1 (Amyloid beta protein- binding protein 1, 59 kDa) (APP-BP1). [Source:Uniprot/SWISSPROT;Acc:Q9Z1A5]" $band [1] "p14" $chromosome [1] "19" $start [1] 382556 $end [1] 408667 $martID [1] "ENSRNOG00000033133" > getGO(id="1387055_at", array="rat230_2",mart=mart) An object of class "martTable" Slot "id": [1] "1387055_at" "1387055_at" "1387055_at" "1387055_at" Slot "table": $GOID [1] "GO:0016874" "GO:0006512" "GO:0006915" "GO:0007049" $description [1] "ligase activity" "ubiquitin cycle" "apoptosis" "cell cycle" $evidence [1] "IEA" "IEA" "IEA" "IEA" $martID [1] "ENSRNOG00000033133" "ENSRNOG00000033133" "ENSRNOG00000033133" [4] "ENSRNOG00000033133" best, Steffen David Kipling wrote: > Hi > > Although I can find the rae230a and rae230b rat annotation metadata > packages on the Bioconductor site, there doesn't seem to be one for > the rat 230 2.0 chip (which is the combination of rae230a and rae230b). > > Is one available anywhere, and if not what would be the easiest way to > make one (e.g. is is feasible to merge the two existing packages)? > > Many thanks > > David > > Prof David Kipling > Department of Pathology > School of Medicine > Cardiff University > Heath Park > Cardiff CF14 4XN > > Tel: 029 2074 4847 > Email: KiplingD@cardiff.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

David Kipling wrote: > Hi > > Although I can find the rae230a and rae230b rat annotation metadata > packages on the Bioconductor site, there doesn't seem to be one for the > rat 230 2.0 chip (which is the combination of rae230a and rae230b). I see the rat2302 annotation package directly below the two you mention above (on the website). Anyway, going to the website and downloading the package you want is probably the least efficient and most error prone way to do things. Please use the available functions in the reposTools package, which will automagically get the correct package for your particular version of R (not that critical here, but true in a general sense). library(reposTools) install.packages2("rat2302") Will get you what you want. Note that it is not always obvious what the name of the package will be, especially given Affy's complete inability to keep consistent naming standards. If you know the name that Affy has given the chip, then the package names are obvious; simply convert to lowercase and strip out any punctuation cruft that may be in the name (spaces, underscores, hyphens, dots, slashes, smiley faces... hey you never know with affy ;-D) e.g., the chip name in this case is the Rat 230_2, so the annotation package will be rat2302, the probe package will be rat2302probe, and the cdfenv will be rat2302cdf. HTH, Jim > > Is one available anywhere, and if not what would be the easiest way to > make one (e.g. is is feasible to merge the two existing packages)? > > Many thanks > > David > > Prof David Kipling > Department of Pathology > School of Medicine > Cardiff University > Heath Park > Cardiff CF14 4XN > > Tel: 029 2074 4847 > Email: KiplingD@cardiff.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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