[BioC] mapping probe sets from yeast2 array to probe sets in hgu133A

[Glazko, Galina]

Dear Alexandre, James and list

thank you very much for your helpful advises!
Alexandre, I am very grateful for these mappings, 

best
Galina

________________________________________
From: Alexandre Kuhn [kuhnam at mail.nih.gov]
Sent: Tuesday, August 10, 2010 6:00 PM
To: Glazko, Galina; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A

Hi Galina, you can use the function ps2ps in the package annotationTools.
You will only need to download the Affymetrix annotation files corresponding
to your microarrays of interest, as well as the HomoloGene database (see FTP
site on http://www.ncbi.nlm.nih.gov/homologene). You can then do

annotYeast <-
read.csv('Yeast_2.na30.annot.csv',colClasses='character',comment.char='#')
annotHuman <-
read.csv('HG-U133A.na30.annot.csv',colClasses='character',comment.char='#')
homologene <- read.delim('homologene_build64.data',header=FALSE)
homoSapiens_ID <- 9606
mappingTable <- ps2ps(annotYeast,annotHuman,homologene,homoSapiens_ID)

Alternatively, if you want to make use of the probe set mapping provided by
Affymetrix, you can also use the function getHOMOLOG to mine the
corresponding file

affyOrthologs <-
read.csv("Yeast_2.na30.ortholog.csv",colClasses='character')
allps <- annotYeast[,1]
affyMap <-
getHOMOLOG(allps,'HG-U133A',affyOrthologs,cluster=TRUE,clusterCol=1,speciesC
ol=4,idCol=3)

In this particular yeast to human mapping, the number of human ortholog
probe sets found with the Affymetrix ortholog file (2656) is much higher
than with ps2ps (1405). The reason seems to be that some probe sets have an
empty "Entrez gene ID" entry in the Yeast2 annotation file (gene symbols are
present though). This prevents ps2ps from mapping these probe sets since it
uses Entrez gene IDs to find orthologs in HomoloGene.

Alexandre


> -----Original Message-----
> From: Glazko, Galina [mailto:Galina_Glazko at urmc.rochester.edu]
> Sent: Thursday, August 05, 2010 2:42 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] mapping probe sets from yeast2 array to probe sets in
> hgu133A
>
> Dear List,
>
> I would appreciate if someone could indicate the easy way how to map
> probe
> sets from yeast2 array onto hgu133a probe sets in Bioconductor;
> May be throughout BioMart?
> (Mapping should be based on orthologs).
>
> I know how to do it in NetAffx, Affymetrix but it takes too much time.
> Thank you!
>
> Best regards
> Galina
>
>
>       [[alternative HTML version deleted]]
>
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