[BioC] Mapping Agilent Probes

[Peter Robinson]

Dear 'conductors,

I am trying to get a mapping from Agilent mouse microarray probes to 
ENSEMBL gene ids for further analysis.

 >library("mgug4122a.db")
 >data = "path to data"  ## This is data produced from an initial 
analysis of an Agilent hybridization
 >dat <-read.table(data,sep=",",header=TRUE)
 >pro = as.character(dat[,3])   ### The Agilent probe names

 > head(pro)
[1] "A_52_P616356" "A_52_P580582" "A_52_P403405" "A_52_P819156" 
"A_51_P331831"
[6] "A_51_P430630"


 >ens = unlist(mget(pro,mgug4122aENSEMBL))

 >map.dat = 
merge(dat,ens,by=intersect(dat[,3],names(ens)),all.x=TRUE,all.y=FALSE)
Fehler in fix.by(by.x, x) : 'by' muss gültige Spalte(n) spezifizieren

Thus I get an error stating that 'by' needs to specify a valid column.


My goal is to create a table that I can output that will contain the 
original information as well as the mapping to ENSEMBL in the correct rows.

Also, what is the meaning of ENSEMBL2probe in the  "mgug4122a.db" package?

Is it worrisome that there seems to be an ENSEMBL id for only about 80% 
of the Agilent probes? Is there any way of getting more mappings? (I am 
aware that many of the probes are controls).

THanks Peter