[BioC] export expression set from beadarray

Matthew Vitalone matthew_vitalone at wmi.usyd.edu.au
Tue Oct 7 08:20:24 CEST 2008

Hi all,

How do I get my normalised Illumina data , via bead array, exported into 
a expression set as a tab delimited .txt file ? I have tried following 
the notes on the bioconductor website and anything else I can find on 
the web. I have also looked through previous posts and I have no been 
able to find the answer. I am not use to beadarray or any command line 
type analysis.

Thanks you so much for you help.

Here is my code: (running R2.7.2, and the latest version of beadarray)



**BSData = readBeadSummaryData("expset-all.txt", qcFile=NULL, 
sampleSheet=NULL,sep="\t",skip=8, ProbeID="PROBE_ID", columns = 
list(exprs = "AVG_Signal", se.exprs="BEAD_STDERR", NoBeads = 
"Avg_NBEADS", Detection="Detection Pval"), dec=".")



*BSData.log2.qspline = normaliseIllumina(BSData, method="qspline", 


eSet = new("ExpressionSet", assayData= 
    *Error in function (classes, fdef, mtable)  :
      unable to find an inherited method for function "exprs", for 
signature "NULL"

What is wrong with this final above comand that causes the error?

Matthew Vitalone B.Sc (Hons) PhD(progress)
NHMRC Centre for Clinical Research Excellence in Renal Medicine
Centre For Transplant and Renal Research
Transplant Laboratory (Room 2175), Clinical Sciences
Westmead Millennium Institute
Darcy Road, Westmead, NSW, 2145.
Sydney, Australia.

Phone: (+61-2) 9845 8906
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Fax: (+61-2) 9633 9351
Email: matthew_vitalone at wmi.usyd.edu.au 

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