[BioC] probe to entrezID mapping with aafLocusLink

[Merja Heinaniemi]

Hi!

I was mapping probeIDs from 133plus2 arrays to entrezIDs using aafLocusLink, some months ago with an earlier version of the package, and now with the current annaffy and hgu133plus2 packages. I compared my results and some probes no longer got mapped with the new package version, e.g POU5F1. The gene does have probes on the array, all just happen to be x_at probes. So I thought maybe all those less specific probes lack entrez mappings but another gene with x_at does have a matching entrezID. So why is e.g POU5F1 missing one? I include below the R code that can be used to reproduce my problem (even the first part if any hgu133Plus2 arrays are read in), sessionInfo is given at the end.

And more importantly, how do I get such probes mapped to an entrezID using Bioconductor? I was assuming the hgu133plus2 package contains all manufacturer annotations so I should find a match, or am I wrong?

thanks in advance!

Merja



##R commands:

#affybatch=read.affybatch(filenames=Filenames)
#eset=rma(affybatch)
#grep("208286_x_at",featureNames(eset))
#[1] 17711

library(annaffy)
library(hgu133plus2.db)
probeID1="208286_x_at" ##this is POU5F1 entrezID 5460
probeID2="215600_x_at"  ##this is FBXW12 entrezID 285231
entrezID1=aafLocusLink(probeID1, "hgu133plus2.db")
entrezID1
#integer()
entrezID2=aafLocusLink(probeID2, "hgu133plus2.db")
entrezID2
#[1] 285231

x <- hgu133plus2ENTREZID
## Get the probe identifiers that are mapped to an ENTREZ Gene ID
mapped_probes <- mappedkeys(x)
## Convert to a list
xx <- as.list(x[mapped_probes])
xx[xx=="5460"]
#list()
xx[xx=="285231"]
#$`1564138_at`
#[1] "285231"

#$`215600_x_at`
#[1] "285231"

> sessionInfo()
#R version 2.10.0 (2009-10-26)
#i386-apple-darwin9.8.0

#locale:
#[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

#other attached packages:
# [1] hgu133plus2cdf_2.5.0 hgu133plus2.db_2.3.5 org.Hs.eg.db_2.3.6   annaffy_1.18.0       KEGG.db_2.3.5        GO.db_2.3.5
# [7] RSQLite_0.7-3        DBI_0.2-4            AnnotationDbi_1.8.1  affy_1.24.2          Biobase_2.6.0

#loaded via a namespace (and not attached):
#[1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.0