Create ExpressionSet object in R from Illumina Beadarray Data

eset_from_beadarray.r

## Stephen Turner
## University of Virginia Bioinformatics Core
## November 28, 2012

## Useful references:
# http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002276
# http://www.bioconductor.org/help/course-materials/2007/BioC2007/labs/beadarray/BioC2007_beadarray_slides.pdf
# http://www.bioconductor.org/help/course-materials/2007/BioC2007/labs/beadarray/beadarrayBioc07.pdf
 
## Instructions:
#
# This is a description of how to get Illumina array data from genome studio to R
# using GenomeStudio.
# 
# The raw data comes in a directory which includes two subdirectories: “DeCode
# Data” and “Image Directory”.
# 
# First open genome studio and create a new Gene Expression project. The dialog
# that pops-up asks for a specification of the gene expression assay type.
# Selected Direct Hyb. You are then asked to define the path to the projects
# repository directory and the project name. Select the Image Directory of your
# data as a repository. You can select the samples you are interested in from the
# array list. Note that you can group samples into groups of replicates, but I
# skip this part, i.e, I leave them ungrouped (do this later in limma). Finish by
# generating the summaries. Note that according to the beadarray vignette you
# should select no background correction.
# 
# First we create the “SampleProbeProfile.txt” as follows:
# 
# Select the Sample Probe Profile Tab and use the Column Chooser to select the
# ProbeID column and the following columns: AVG_Signal, BEAD_STDERR, Avg_NBEADS,
# Detection Pval. Save the file as “SampleProbeProfile.txt”.
# 
# Follow the same procedure on the Control Probe Profile tab (lower left panel)
# and save the output file as: “ControlProbeProfile.txt”.
# 
# Now we have the data we need to use the beadarray package.

library(annotate)
library(beadarray)
library(limma)
library(illuminaMousev2.db)

## The data file from GenomeStudio
dataFile="/path/to/SampleProbeProfile.txt"

## The control file from GenomeStudio
qcFile="/path/to//ControlProbeProfile.txt"

## Reading in the file and creating ExpressionSetIllumina object
eset=readBeadSummaryData(dataFile=dataFile, qcFile=qcFile, 
                             ProbeID="PROBE_ID", controlID="ProbeID", 
                             skip=0, qc.skip=0,
                             annoCols=c("TargetID", "PROBE_ID","SYMBOL"))

## Now continue on with your normal analysis with limma package and annotation with annotate package

Hi,

I am facing some problems creating expression set object from bead array. I am doing exactly the same thing but it is giving me the following error.

Error in row.names<-.data.frame(*tmp*, value = value) :
invalid 'row.names' length

Do you have some idea how this can be solved?

Thanks,

Yogesh