[BioC] How to use ExpressionSet for further Analysis

Md.Mamunur Rashid mamunur.rashid at kcl.ac.uk
Mon Jul 27 17:33:15 CEST 2009

Dear Members,

I am very new to both R and bioconductor. I am working with illumina 
microarray data from ArrayExpress. (E-TABM-421, it's in the proivate 
section. so may not accessible to everyone).
I have downloaded the processed zip file, .adrf , .sdrf, .idf files from 
the directory. Using the Arrayexpress "procset" method I have managed to 
create an ExpressionSet object.


1. Now I am not sure how can I use this ExpressionSet object for further 
analysis of the Data?
2. Is it possible to convert this ExpressionSet object to object of some 
other classes (i.e. Lumi)?
3. If possible can you please show a simple example ?

I would like to thanks in advance for any sort of help and suggestion.

Md.Mamunur Rashid

below is the R script I have used and few results:

 > library(ArrayExpress)
 > etabm421 <- list(path = ".",rawadata = NULL, rawfiles = NULL, 
procdata = "E-TABM-421.processed.zip",procfile = 
"E-TABM-421-processed-data-1583036605.txt",sdrf = "E-TABM-421.sdrf.txt", 
idf = "E-TABM-421.idf.txt", adf = "A-MEXP-931.adf.txt")
 > cn = getcolproc(ETABM421)
 > cn
[1] "Reporter REF"              "BeadStudio:AVG_Signal"   
[3] "BeadStudio:Detection Pval"
 > proset = procset(ETABM421,cn[2])

 > slotNames(proset)
[1] "assayData"         "phenoData"         "featureData"       
[5] "annotation"        ".__classVersion__"

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