[BioC] Mapping Agilent Probes
marten.jaeger at charite.de
Sat Jul 18 21:11:41 CEST 2009
you can use the annotate package:
>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.
> Dear 'conductors,
> I am trying to get a mapping from Agilent mouse microarray probes to
> ENSEMBL gene ids for further analysis.
> >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)
>  "A_52_P616356" "A_52_P580582" "A_52_P403405" "A_52_P819156"
>  "A_51_P430630"
> >ens = unlist(mget(pro,mgug4122aENSEMBL))
> >map.dat =
> 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
> Also, what is the meaning of ENSEMBL2probe in the "mgug4122a.db"
> 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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