I ran into an oddity that I thought others working with hgu133plus2 chips might want to know. hgu133plus2SYMBOL is missing an entry for 211506_s_at. >library(annaffy) >library(hgu133plus2) >library(hgu133plus2cdf) >library(hgu133plus2probe) >probeids <- ls(hgu133plus2SYMBOL) > probeids[20834] [1] "211506_s_at" > getText(aafSymbol(probeids[20834], "hgu133plus2")) [1] "" But the netaffx website shows the Gene Symbol for 211506_s_at as IL8. Here's my setup: base 2.0.1 datasets 2.0.1 utils 2.0.1 grDevices 2.0.1 graphics 2.0.1 stats 2.0.1 methods 2.0.1 tools 2.0.1 Biobase 1.5.0 reposTools 1.5.1 affy 1.5.8 GO 1.6.8 KEGG 1.6.8 annotate 1.5.1 annaffy 1.0.11 hgu133plus2 1.6.8 nlme 3.1-53 hgu133plus2cdf 1.4.3 xtable 1.2-4 matchprobes 1.0.12 hgu133plus2probe 1.0 Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html

Hi Dick, The affy annotation is correct. I'm working on an alternative Bioconductor package (biomaRt) that can be used for annotation and retrieves the annotation directly from Ensembl (http://www.ensembl.org). You can find the biomaRt package in the developmental packages if you want to give it a try. This is what it returned for your query: >library(biomaRt) > mart<-martConnect() - Connected to ensembl_mart_28_1, vega_mart_28_1, snp_mart_28_1 and sequence_mart_28_1 - > getGene(id="211506_s_at",array="hgu133plus2",mart=mart) An object of class "martTable" Slot "id": [1] "211506_s_at" Slot "table": $symbol [1] "IL8" $description [1] "Interleukin-8 precursor (IL-8) (CXCL8) (Monocyte-derived neutrophil chemotactic factor) (MDNCF) (T-cell chemotactic factor) (Neutrophil- activating protein 1) (NAP-1) (Protein 3-10C) (Granulocyte chemotactic protein 1) (GCP-1) (Monocyte derived neutrophil activating peptide) (MONAP) (Emoctakin) [Contains: MDNCF-a (IL8/NAP1 form I) (GCP/IL-8 protein IV); IL-8(1-77) (MDNCF-b) (IL8/NAP1 form II) (GCP/IL-8 protein II) ((ala-IL-8)77); IL-8(6-77) (Lymphocyte-derived neutrophil- activating factor) (LYNAP) (Neutrophil-activating factor) (NAF) (MDNCF-c) (IL8/NAP1 form III) (GCP/IL-8 protein I) ((ser-IL-8)72); IL- 8(7-77) (IL8/NAP1 form IV) (GCP/IL-8 protein V); IL-8(8-77) (IL8/NAP1 form V) (GCP/IL-8 protein VI); IL-8(9-77) (IL8/NAP1 form VI) (GCP/IL-8 protein III)]. [Source:Uniprot/SWISSPROT;Acc:P10145]" $band [1] "q13.3" $chromosome [1] "4" $start [1] 74971310 $end [1] 74974466 $martID [1] "ENSG00000169429" Cheers, Steffen I ran into an oddity that I thought others working with hgu133plus2 chips might want to know. hgu133plus2SYMBOL is missing an entry for 211506_s_at. > library(annaffy) > library(hgu133plus2) > library(hgu133plus2cdf) > library(hgu133plus2probe) > probeids <- ls(hgu133plus2SYMBOL) > probeids[20834] [1] "211506_s_at" > getText(aafSymbol(probeids[20834], "hgu133plus2")) [1] "" But the netaffx website shows the Gene Symbol for 211506_s_at as IL8. Here's my setup: base 2.0.1 datasets 2.0.1 utils 2.0.1 grDevices 2.0.1 graphics 2.0.1 stats 2.0.1 methods 2.0.1 tools 2.0.1 Biobase 1.5.0 reposTools 1.5.1 affy 1.5.8 GO 1.6.8 KEGG 1.6.8 annotate 1.5.1 annaffy 1.0.11 hgu133plus2 1.6.8 nlme 3.1-53 hgu133plus2cdf 1.4.3 xtable 1.2-4 matchprobes 1.0.12 hgu133plus2probe 1.0 Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Dick, I had a chat with our annotation expert and wanted to report back what I learned. On Mar 2, 2005, at 10:06 AM, Dick Beyer wrote: > I ran into an oddity that I thought others working with hgu133plus2 > chips might want to know. > > hgu133plus2SYMBOL is missing an entry for 211506_s_at. > As I understand it, when this data package was created the netaffx database was not available and a match for the Affy ID you've identified was not found in the public domain databases. In the next version of this package we will be able to include information from the netaffx database. Thanks for pointing this out. + seth