createESET: Create a Bioconductor ExpressionSet

Description

Given the identifier of a GEO series (GSE) record creates one or more ExpressionSets from the data loaded in the compendium database

Usage

createESET(con, GSEid, GPLid = "", parsing = TRUE)

Arguments

con

list containing a connection object specifying the user name and password to connect or interact with the compendium database (see connectDatabase)

GSEid

character string specifying the GSE ID to be converted to one or more ExpressionSets

GPLid

character string specifying the GPL ID. The default value is "", in which case a separate ExpressionSet will be created for each of the GPLs in the GSE specified by GSEid.

parsing

logical, if set to its default value (TRUE) the phenotypic data of the samples as available in the sample characteristics extracted from GEO will be parsed into separate columns.

Value

A list with components of class ExpressionSet (from the Biobase Bioconductor package). Each ExpressionSet is named according to the GSEid with its corresponding GPL ID(s). If a GSE consists of GSMs with a different number of features, multiple ExpressionSets are created such that GSMs with the same features are grouped into one ExpressionSet.

Details

This function generates one or more ExpressionSets for the specified GSE from the data loaded in the compendium database. Each ExpressionSet contains an assayData slot with all data related to the expression measurements parsed from a GSE SOFT file. Probe annotation is provided in the featureData slot with all data parsed from the most recent annotation file provided for the corresponding GPL (if available at ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/annotation/platforms/). Sample annotation is provided in the phenoData slot and obtained by parsing the output of the function GSMdescriptions.

Examples

Run this code

 ## Not run: 
#   conn <- connectDatabase(dbname="compendium")
# 
#   # Create ExpressionSet for the samples in GSE1657 corresponding to GPL96
#   esets <- createESET(conn,"GSE1657","GPL96")
#   # esets contains one component: "esetGSE1657_GPL96_SC"
# 
#   # Create ExpressionSet for the samples of both platforms present in GSE1657 (GPL96 & 
#   # GPL97), i.e, set GPLid to default value
#   esets <- createESET(conn,"GSE1657") # Default GPLid=""
#   # esets contains two components: "esetGSE1657_GPL96_SC" and "esetGSE1657_GPL97_SC"
#  ## End(Not run)