R Packages (CDFs)
This page provides a series of R packages, designed to be used with BioConductor tools, that allow to apply in a simple way the PROBE MAPPING data included in GATExplorer. The R scripts below can be used to perform a microarray expression calculation according to the re-mapping data.
The R packages are built as custom Chip Definition Files (CDFs) that contain for each microarray model all the information about the specific mapping of the oligo probes to genes, to transcripts or to exons from Ensembl (i.e. ENSGx, ENSTx or ENSEx). The files are called GeneMapper, TranscriptMapper and ExonMapper. Another type of files called ncRNA Mapper include the probes that do not map to any coding region (i.e. do not map in protein-coding exons) but that were mapped to a database for non-coding RNA (ncRNA) of human and mouse (derived from RNAdb).
Therefore, the tables below include the R packages corresponding to 4 different levels of mapping for each microarray:
GeneMapper: include the groups of unambiguous probes that map to each specific gene.
TranscriptMapper: include the groups of unambiguous probes that map to each specific transcript.
ExonMapper: include the groups of unambiguous probes that map to each specific exon.
ncRNA Mapper: include the groups of probes that did not map any protein-coding exon but map on ncRNAs.
(Each group should include at least a minimum of 3 probes mapping in the corresponding entity)
These files can be downloaded and they must be installed in R like any other R package.
Please, refer to GATExplorer as source.

The following examples show how to use the mapping packages in R with some BioConductor libraries and tools:
library(affy);   # Load the "affy" library from BioConductor.
cel <- ReadAffy();   # Read the microarray .CEL files present in this folder, creating R expression objects.
cel@cdfName <- "genemapperhgu133a";   # Set the CDF (Chip Definition File) to the new "GeneMapper" file provided.
expression_output <- rma(cel);   # Calculate the expression signal using RMA algorithm.
library(affy);   # Load the "affy" library from BioConductor.
expression_output <- justRMA(cdfname="genemapperhgu133a"); # Directly apply justRMA and the new CDF.
• Go to Gene, Transcript and Exon CDF packages (LINUX version)
• Go to Gene, Transcript and Exon CDF packages (WINDOWS version)
• Go to ncRNA CDF packages (LINUX version)
• Go to ncRNA CDF packages (WINDOWS version)
Example of how to install a CDF package (in LINUX command line).
R CMD INSTALL genemapperhgu133acdf_1.0.tar.gz
Gene, Transcript and Exon CDF packages (LINUX version)
Microarray Probes to Gene Loci Probes to Transcripts
Human
HG_U133A GeneMapper TranscriptMapper
HG_U133A_2 GeneMapper TranscriptMapper
HG_U133B GeneMapper TranscriptMapper
HG_U133_Plus_2 GeneMapper TranscriptMapper
HG_U95A GeneMapper TranscriptMapper
HG_U95Av2 GeneMapper TranscriptMapper
HG_U95B GeneMapper TranscriptMapper
HG_U95C GeneMapper TranscriptMapper
HG_U95D GeneMapper TranscriptMapper
HG_U95E GeneMapper TranscriptMapper
HG_Focus GeneMapper TranscriptMapper
HC_G110 GeneMapper TranscriptMapper
U133_X3P GeneMapper TranscriptMapper
Human_Gene_1.0 GeneMapper TranscriptMapper
Human_Exon_1.0 GeneMapper TranscriptMapper
Mouse
MG_U74A GeneMapper TranscriptMapper
MG_U74Av2 GeneMapper TranscriptMapper
MG_U74B GeneMapper TranscriptMapper
MG_U74Bv2 GeneMapper TranscriptMapper
MG_U74C GeneMapper TranscriptMapper
MG_U74Cv2 GeneMapper TranscriptMapper
Mouse430_2 GeneMapper TranscriptMapper
Mouse430A_2 GeneMapper TranscriptMapper
MOE430A GeneMapper TranscriptMapper
MOE430B GeneMapper TranscriptMapper
Mu11KsubA GeneMapper TranscriptMapper
Mu11KsubB GeneMapper TranscriptMapper
Mouse_Gene_1.0 GeneMapper TranscriptMapper
Mouse_Exon_1.0 GeneMapper TranscriptMapper
Rat
RG_U34A GeneMapper TranscriptMapper
RG_U34B GeneMapper TranscriptMapper
RG_U34C GeneMapper TranscriptMapper
Rat230_2 GeneMapper TranscriptMapper
RAE230A GeneMapper TranscriptMapper
RAE230B GeneMapper TranscriptMapper
RN_U34 GeneMapper TranscriptMapper
RT_U34 GeneMapper TranscriptMapper
Rat_Gene_1.0 GeneMapper TranscriptMapper
Rat_Exon_1.0 GeneMapper TranscriptMapper
Human_Exon_1.0 Mouse_Exon_1.0 Rat_Exon_1.0
ExonMapper ExonMapper ExonMapper
Gene, Transcript and Exon CDF packages (WINDOWS version)
Microarray Probes to Gene Loci Probes to Transcripts
Human
HG_U133A GeneMapper TranscriptMapper
HG_U133A_2 GeneMapper TranscriptMapper
HG_U133B GeneMapper TranscriptMapper
HG_U133_Plus_2 GeneMapper TranscriptMapper
HG_U95A GeneMapper TranscriptMapper
HG_U95Av2 GeneMapper TranscriptMapper
HG_U95B GeneMapper TranscriptMapper
HG_U95C GeneMapper TranscriptMapper
HG_U95D GeneMapper TranscriptMapper
HG_U95E GeneMapper TranscriptMapper
HG_Focus GeneMapper TranscriptMapper
HC_G110 GeneMapper TranscriptMapper
U133_X3P GeneMapper TranscriptMapper
Human_Gene_1.0 GeneMapper TranscriptMapper
Human_Exon_1.0 GeneMapper TranscriptMapper
Mouse
MG_U74A GeneMapper TranscriptMapper
MG_U74Av2 GeneMapper TranscriptMapper
MG_U74B GeneMapper TranscriptMapper
MG_U74Bv2 GeneMapper TranscriptMapper
MG_U74C GeneMapper TranscriptMapper
MG_U74Cv2 GeneMapper TranscriptMapper
Mouse430_2 GeneMapper TranscriptMapper
Mouse430A_2 GeneMapper TranscriptMapper
MOE430A GeneMapper TranscriptMapper
MOE430B GeneMapper TranscriptMapper
Mu11KsubA GeneMapper TranscriptMapper
Mu11KsubB GeneMapper TranscriptMapper
Mouse_Gene_1.0 GeneMapper TranscriptMapper
Mouse_Exon_1.0 GeneMapper TranscriptMapper
Rat
RG_U34A GeneMapper TranscriptMapper
RG_U34B GeneMapper TranscriptMapper
RG_U34C GeneMapper TranscriptMapper
Rat230_2 GeneMapper TranscriptMapper
RAE230A GeneMapper TranscriptMapper
RAE230B GeneMapper TranscriptMapper
RN_U34 GeneMapper TranscriptMapper
RT_U34 GeneMapper TranscriptMapper
Rat_Gene_1.0 GeneMapper TranscriptMapper
Rat_Exon_1.0 GeneMapper TranscriptMapper
Human_Exon_1.0 Mouse_Exon_1.0 Rat_Exon_1.0
ExonMapper ExonMapper ExonMapper
ncRNA CDF packages (LINUX version)
Microarray Probes to ncRNA
Human
HG_U133A ncRNA Mapper
HG_U133A_2 ncRNA Mapper
HG_U133B ncRNA Mapper
HG_U133_Plus_2 ncRNA Mapper
HG_U95A ncRNA Mapper
HG_U95Av2 ncRNA Mapper
HG_U95B ncRNA Mapper
HG_U95C ncRNA Mapper
HG_U95D ncRNA Mapper
HG_U95E ncRNA Mapper
HG_Focus ncRNA Mapper
HC_G110 ncRNA Mapper
U133_X3P ncRNA Mapper
Human_Gene_1.0 ncRNA Mapper
Human_Exon_1.0 ncRNA Mapper
Mouse
MG_U74A ncRNA Mapper
MG_U74Av2 ncRNA Mapper
MG_U74B ncRNA Mapper
MG_U74Bv2 ncRNA Mapper
MG_U74C ncRNA Mapper
MG_U74Cv2 ncRNA Mapper
Mouse430_2 ncRNA Mapper
Mouse430A_2 ncRNA Mapper
MOE430A ncRNA Mapper
MOE430B ncRNA Mapper
Mu11KsubA ncRNA Mapper
Mu11KsubB ncRNA Mapper
Mouse_Gene_1.0 ncRNA Mapper
Mouse_Exon_1.0 ncRNA Mapper
ncRNA CDF packages (WINDOWS version)
Microarray Probes to ncRNA
Human
HG_U133A ncRNA Mapper
HG_U133A_2 ncRNA Mapper
HG_U133B ncRNA Mapper
HG_U133_Plus_2 ncRNA Mapper
HG_U95A ncRNA Mapper
HG_U95Av2 ncRNA Mapper
HG_U95B ncRNA Mapper
HG_U95C ncRNA Mapper
HG_U95D ncRNA Mapper
HG_U95E ncRNA Mapper
HG_Focus ncRNA Mapper
HC_G110 ncRNA Mapper
U133_X3P ncRNA Mapper
Human_Gene_1.0 ncRNA Mapper
Human_Exon_1.0 ncRNA Mapper
Mouse
MG_U74A ncRNA Mapper
MG_U74Av2 ncRNA Mapper
MG_U74B ncRNA Mapper
MG_U74Bv2 ncRNA Mapper
MG_U74C ncRNA Mapper
MG_U74Cv2 ncRNA Mapper
Mouse430_2 ncRNA Mapper
Mouse430A_2 ncRNA Mapper
MOE430A ncRNA Mapper
MOE430B ncRNA Mapper
Mu11KsubA ncRNA Mapper
Mu11KsubB ncRNA Mapper
Mouse_Gene_1.0 ncRNA Mapper
Mouse_Exon_1.0 ncRNA Mapper