Dear all,

I am trying to look at a relatively old mouse data that was taken using Expression Chip v6.1.1. The problem came I when I tried to convert Probe IDs to gene names. Probe IDs are, for example: 10243, 10280, 10575, 20048, ..., 102900072, 102900075, ...

I tried an old keys/mapIds way using 3 packages: illuminaMousev1.db, illuminaMousev1.1.db, illuminaMousev2.db and none had Probe IDs similar to what I got from GEO file

As an example of how I did it:

toget <- c("GENENAME","SYMBOL","ENTREZID","ENSEMBL", "ACCNUM")

library("illuminaMousev1.db")

ks <- keys(illuminaMousev1.db)

annData1 <- as.data.frame(lapply(toget, function(x) mapIds(illuminaMousev1.db, ks, x, "PROBEID")))

I eventually (possibly) succeeded using 

genes <- probeID2nuID(probes, lib.mapping = "lumiMouseIDMapping"[,"Symbol"]

from lumi (I was using lumi for reading/normalizing anyway), but when I started investigating duplicate gene entries and presumably transcript variants, I felt a need to double check the conversion. Does anybody have a suggestion?

By the way, when I try

getSYMBOL(380091,"lumiMouseIDMapping")

(380091 being a probe ID for one of genes with name repeated multiple times and with different, according to google, transcript variants) I get

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘columns’ for signature ‘"function"’

Thank you 

Hi Smt8n,

Those look to me to be ArrayAddressIDs that are in illuminaMousev1p1.db. An (inelegant) approach to extracting them would be:

library("illuminaMousev1p1.db")

library(DBI)

fullanno<-illuminaMousev1p1fullReannotation()
fullanno[fullanno$ArrayAddress %in% c(10243, 10280, 10575, 20048, 102900072, 102900075),c(2,12,13,16)]
      ArrayAddress           GenomicLocation SymbolReannotated EnsemblReannotated
3222     102900075  chr6:31372368:31372417:+          AK052154               <NA>
3934     102900072 chr11:62141678:62141727:+             Ncor1 ENSMUSG00000042298
9122         10280 chr11:99712245:99712294:-         Krtap4-16 ENSMUSG00000046474
16521        20048  chr7:31455862:31455911:-     4930479M11Rik ENSMUSG00000049761
19514        10575 chr13:73819014:73819063:-           Slc6a19 ENSMUSG00000021565
20442        10243  chr5:34839459:34839508:-             Tnip2 ENSMUSG00000059866

I hope that helps.

Andy