On 4/19/2013 9:25 AM, Robert Castelo wrote: > hi, > > if you're searching from something readily available in R, you can try > to do following: > > library(BiocInstaller) ## assuming you installed some BioC package once > biocLite("tweeDEseqCountData") > > library(tweeDEseqCountData) > data(hkGenes) > length(hkGenes) > [1] 669 > head(hkGenes) > [1] "ENSG00000149925" "ENSG00000102144" "ENSG00000142676" > "ENSG00000108298" > [5] "ENSG00000144713" "ENSG00000075624" > > check out the help page of 'hkGenes' for the source publication of > this list. > > as you see, these are Ensmbl gene identifiers, but if you need Affy > IDs from a particular Affy chip, let's say HG-U133 Plus 2.0, you can > use the great identifier mapping functionality of the package > GSEABase, which in principle is designed to map identifier between > gene sets and ExpressionSet objects, but which you can tweak to do > this job for you passing the housekeeping gene list as if it were one > gene set: > > library(GSEABase) > > dummygs <- GeneSet(hkGenes, geneIdType=ENSEMBLIdentifier()) > > hkGenesHGU133plus2AffyIDs <- geneIds(mapIdentifiers(dummygs, > AnnoOrEntrezIdentifier("hgu133plus2"))) > > length(hkGenesHGU133plus2AffyIDs) > [1] 1263 > > head(hkGenesHGU133plus2AffyIDs) > [1] "200966_x_at" "214687_x_at" "238996_x_at" "1558365_at" "200737_at" > [6] "200738_s_at" Or you could use more direct methods: library(hgu133plus2.db) mapped.genes <- select(hgu133plus2.db, hkGenes, "PROBEID", "ENSEMBL") head(mapped.genes) ENSEMBL PROBEID 1 ENSG00000149925 200966_x_at 2 ENSG00000149925 214687_x_at 3 ENSG00000149925 238996_x_at 4 ENSG00000102144 1558365_at 5 ENSG00000102144 200737_at 6 ENSG00000102144 200738_s_at Best, Jim > > > cheers, > robert. > > > On 04/18/2013 02:03 AM, Jack Luo wrote: >> Not sure whether it's an appropriate question for Bioconductor. Is >> there a >> place to find a list of housekeeping genes (identified by Affy)? >> >> Thanks, >> >> -Jack >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099