map.data: Probe-set Mapping Data

In AGDEX: Agreement of Differential Expression Analysis

Description

A mapping between Human probe-sets and Mouse probe-sets

Usage

data(map.data)

Details

map.data is a list object containing 3 components, probe.map, map.Aprobe.col and map.Bprobe.col. The component probe.map is a data frame with 2 columns of probe-sets identifiers from human and mouse array respectively. This sample mapping data probe.map is a subset of the full mapping data set across human genome U133 Plus 2.0 Array and mouse Expression 430 Array available at www.affymetrix.com. They provide mutiple match mode data sets, such as Good Match, Complex Match Best match etc. We downloaded the Best Match data set as our mapping data. The probe-sets in probe.map are selected such that they are contained in both expression matrix of human.data and mouse.data. Users can choose mapping data according to the species and platforms of their gene expression profiles either by downloading from www.affymetrix.com or from other sources. The array platforms of mapping data must match that of gene expression profile of each species.

probe.map component of the sample data map.data contains 490 rows of ortholog-matched probe-sets across human array and mouse array. map.Aprobe.col and map.Bprobe.col specify column number or name containing the probe-sets from study A and study B respectively.

Value

probe.map	A data frame with 490 rows and 2 columns of probe-sets identifiers of human and mouse
map.Aprobe.col	Column number or name in data frame probe.map containing probe-sets IDs from study A
map.Bprobel.col	Column number or name in data frame probe.map containing probe-sets IDs from study B

See Also

agdex; human.data; mouse.data; gset.data

Examples

# download the "best match" mapping data across human array and mouse array # 
## Not run: 
 map.url <- "http://www.affymetrix.com/Auth/analysis/downloads/na31/ivt/Mouse430_2.na31.ortholog.csv.zip"
 map.file.name <- unlist(strsplit(map.url,split="/"))
 map.file.name <- map.file.name[length(map.file.name)]
 map.destination <- paste(local.data.dir,map.file.name,sep="")
 download.file(map.url,map.destination)  # Affy website may need users to register first
 unzip(map.destination)
 affy.ortho.file <- substring(map.destination,1,nchar(map.destination)-4)
 

# read in the mapping data  #
 ortho.data <- read.csv(affy.ortho.file,quote='"',as.is=T)

 keep the probe-sets identifers of human array "HG-U133_Plus_2" only 
 keep.rows <- is.element(ortho.data$Ortholog.Array,"HG-U133_Plus_2")
 ortho.data <- ortho.data[keep.rows,]

 ortho.data <- ortho.data[,c(1,3)]             # keep the columns containg probe-sets only
 ortho.data$Ortholog.Probe.Set <- tolower(ortho.data$Ortholog.Probe.Set)
 
# prepare the list obejct of map data for calling AGDEX routine #
 map.data <- list(probe.map=ortho.data,
                  map.Aprobe.col=2,   # the column index containing human probe-sets IDs in data frame probe.map 
                  map.Bprobe.col=1)   # the column index containing mouse probe-sets IDs in data frame probe.map

## End(Not run)

AGDEX documentation built on Nov. 8, 2020, 8:32 p.m.