Dear Tom & co,

I used getSymbol but retrieved a limited and variable number of 
probes (1-5) with the same name. What could be the reason for this? 
(in the context of >10 MisMatch/PerfectMatch probes for each gene)

Some background:
         We are applying a contrast analysis to a pathological Affy 
micro-array dataset.
The dataset is available in GEO as a series matrix txt file ( 22645 
probes/ 35 samples-http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2240).

         We interrogated the set with the open access R/Bioconductor 
packages (hgu133b and KEGG, annotate).

Short code:
Loading the libraries:
          library(hgu133b.db)
          library(KEGG.db)
          library(annotate)
In particular we wanted to analyse the apoptosis genes from the KEGG 
apoptosis pathway.
         xx <- as.list(hgu133bPATH2PROBE)  Alternatives ?
         xx$'04210' #genes
However when we retrieve the gene names,
          listtemp<-getSYMBOL(xx$'04210',"hgu133b.db")
we get a variable number of probes (1-5) with the same name, see 
appendix below and we do not retrieve all genes from the KEGG pathway.
Though the probes are all apoptosis genes, I did not anticipate 
finding 5 XIAP probes for example.

Any suggestions to resolve this issue (ic the difference between the probes)?


Kind regards,
Kurt

Appendix:
  listtemp<-getSYMBOL(xx$'04210',"hgu133b.db")
  > listtemp
225471_s_at   226156_at   236664_at 
225858_s_at   225859_at   228363_at 235222_x_at
      "AKT2"      "AKT2"      "AKT2"      "XIAP"      "XIAP"   "XIAP" 
      "XIAP"
243026_x_at   237522_at   232660_at   231228_at   232012_at 
231218_at   223518_at
      "XIAP"       "FAS"       "BAD"    "BCL2L1"     "CAPN1" 
"CASP8"      "DFFA"
   228465_at   244383_at   231779_at   231699_at   235980_at 
229392_s_at   229606_at
     "IRAK1"     "IRAK1"     "IRAK2"    "NFKBIA"    "PIK3CA" 
"PIK3R2"    "PPP3CA"
   231304_at   244782_at   235780_at   225000_at   225011_at 
230202_at   241325_at
    "PPP3R2"    "PPP3R2"    "PRKACB"   "PRKAR2A"   "PRKAR2A" "RELA"    "PIK3R3"
   226551_at   227345_at   231775_at 
237367_x_at   239629_at   222880_at 224229_s_at
     "RIPK1" "TNFRSF10D" 
"TNFRSF10A"     "CFLAR"     "CFLAR"    "AKT3"      "AKT3"
   242876_at   227553_at   227645_at   229415_at   244546_at
  "AKT3"    "PIK3R5"    "PIK3R5"      "CYCS"      "CYCS"


 > sessionInfo()
R version 2.7.1 (2008-06-23)
i386-pc-mingw32

locale:
LC_COLLATE=Dutch_Belgium.1252;LC_CTYPE=Dutch_Belgium.1252;LC_MONETARY=Dutch_Belgium.1252;LC_NUMERIC=C;LC_TIME=Dutch_Belgium.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
  [1] annotate_1.18.0      xtable_1.5-2         KEGG.db_2.2.0
  [4] hgu133b.db_2.2.0     AnnotationDbi_1.2.2  RSQLite_0.6-9
  [7] DBI_0.2-4            affy_1.18.2          preprocessCore_1.2.0
[10] affyio_1.8.0         Biobase_2.0.1

/////////////////////////////////////////Archive postings on the 
subject July 2008
getSYMBOL in package annotate is a nice way to handle this.

I found it easier, at least.

Cheers

Tom
On Jul 3, 2008, at 4:31 PM, Peter Robinson wrote:

 > Dear all,
 >
 > I have a list of affymetrix probeset ids from another program and
 > would like to use annaffy to extract the corresponding gene names.
 > I am still something of a novice at R and am probably doing
 > something silly, but found no answer in the package vignette. My
 > script:
 >
 >
 > library(annaffy)
 >
 > dat <- read.table('sign.txt.cdt',header=T)
 > psets<-dat[,3]
 > symbols<-aafSymbol(as.character(psets),"moe430b.db")
 > s<-as.character(symbols)
 >
 > I was surprisied that so few of the probeset ids got identified by
 > this script. WHat am I doing wrong?
 >
 > THanks Peter
 > s<-as.character(symbols)
 > > s
 >  [1] "character(0)"       "character(0)"       "character(0)"
 >  [4] "character(0)"       "character(0)"       "character(0)"
 >  [7] "character(0)"       "character(0)"       "character(0)"
 > [10] "character(0)"       "character(0)"       "character(0)"
 > [13] "character(0)"       "character(0)"       "Egr3"
 > [16] "character(0)"       "character(0)"       "character(0)"
 > [19] "character(0)"       "character(0)"       "character(0)"
 > [22] "character(0)"       "character(0)"       "character(0)"
 > [25] "Irak2"              "character(0)"       "Coq10b"
 > [28] "character(0)"       "BC063749"           "character(0)"
 > [31] "4631422O05Rik"      "character(0)"       "Coq10b"
 > [34] "character(0)"       "character(0)"       "AI452195"
 > [37] "character(0)"       "character(0)"       "character(0)"
 > [40] "Mobkl2a"            "character(0)"       "character(0)"
 >
 > (...snip....)
 >




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