annotationTools (version 1.46.0)

ps2ps: Find orthologous/homologous probe sets across two different Affymetrix microarray formats using HomoloGene

Description

Takes two Affymetrix annotation files, the HomoloGene database, a target species ID and returns a mapping table with homologous/orthologous probe sets.

Usage

ps2ps(annotation_1,annotation_2,homologene,target_species,probesets=NULL)

Arguments

annotation_1

A data.frame with Affymetrix annotation for the source microarray format.

annotation_2

A data.frame with Affymetrix annotation for the target microarray format.

homologene

A data.frame with HomoloGene database.

target_species

The target species identifier (i.e. the species corresponding to the target microarray).

probesets

A vector of probe set identifiers. If not specified, all probe sets on the source microarray format are mapped (default).

Value

mappingTable

A data.frame with four columns and as many rows as there are probe sets in the source annotation. Eache row corresponds to a probe set in the source annotation (column1), the corresponding gene IDs (column 2), the orthologous gene IDs in the target species (column 3), and the probe sets in the target annotation correspondin to the orthologous gene IDs (column 4).

Details

A table of orthologous/homologous probe sets is built by looking up gene IDs (corresponding to the probe sets on the source microarray array) in HomoloGene to find their orthologs, and identifying probe sets in the target microarray that probe the orthologous gene transcripts.

Affymetrix annotation files can be obtained from Affymetrix (http://www.affymetrix.com). A flat file database version can be obtained from HomoloGene (http://www.ncbi.nlm.nih.gov/HomoloGene) Target species ID are defined by the NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/Taxonomy)

Examples

## Not run: 
# ##load Affymetrix annotations
# annotMouse<-read.csv('Mouse430_2_annot.csv',colClasses='character',comment.char='#')
# annotHuman<-read.csv('HG-U133A_annot.csv',colClasses='character',comment.char='#')
# 
# ##load HomoloGene database
# homologene<-read.delim('homologene.data',header=FALSE)
# 
# ##define target species ID 
# homoSapiens_ID<-9609
# 
# ##map all probe sets on mouse array Mouse 430 2.0 to their orthologs on human array HG-U133A
# mappingTable<-ps2ps(annotMouse,annotHuman,homologene,homoSapiens_ID)
# 
# ##write mapping table to disk
# write.table(mappingTable,file='Mouse4302_HGU133A.txt',sep='\t',col.names=T,row.names=F,quote=FALSE)
# 
# ##to map the first 10 probe sets given in the annotation only
# mappingTable<-ps2ps(annotMouse,annotHuman,homologene,targetSpecies,probesets=annotMouse[1:10,1])
# ## End(Not run)