[BioC] Mapping Agilent Probes

[Marten Jäger]

Hi Peter,

you can use the annotate package:

 >library("annotate")
 >library("mgug4122a.db")

 >AGI_ID = c("A_52_P616356", "A_52_P580582", "A_52_P403405", 
"A_52_P819156", "A_51_P331831", "A_51_P430630")
 >agi.ens = lookUp(AGI_ID, "mgug4122a.db", "ENSEMBL")

This will return you a list with the Ensembl GeneIDs in the correct 
order like in AGI_ID. For AGI_IDs with no corresponding Ensembl geneID 
you will get a "NA".

I hope this will solve your Problem.

Marten

> 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
>
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