Hi, 
I want trying to do  background correction to a Beastudio output file but I can't read it into beadarray.
The sample file (.txt) has the following header:

Illumina Inc. BeadStudio version 3.1.7


Normalization = none


Array Content = HumanRef-8_V2_0_R0_11223162_A.bgx.xml


Error Model = none


DateTime = 24/09/2007 3:01 PM


Local Settings = en-AU


 

ProbeID    TargetID ...etc



The R code used and error message:



PD.bstudiofile ='PD Vs Controls Only (n=70)_Sample_Probe_Profile_Nicko edit.txt'

sampleSheet = "HumanRef-8_V2_11223162_B.csv"



PD<-readBeadSummaryData(
    dataFile=PD.bstudiofile,
    sampleSheet=sampleSheet,
    skip=7,
    ProbeID="ProbeID",
    columns = list(   exprs = "AVG_Signal",
                                NoBeads = "Avg_NBEADS",
                                Detection="Detection",
                                BeadStDev="BEAD_STDEV"))

Error in assayData(BSData)[[index]] = as.matrix(data[[i]]) : 
  attempt to select less than one element



I've checked everything, tried different skip values, etc, with no luck!

Please help me get this data loaded! sample information is



sessionInfo()

R version 2.7.1 (2008-06-23) 

i486-pc-linux-gnu 



attached base packages:

[1] tools     stats     graphics  grDevices utils     datasets  methods  

[8] base     



other attached packages:

 [1] beadarray_1.8.0      affy_1.18.2          preprocessCore_1.2.0

 [4] affyio_1.8.0         geneplotter_1.18.0   annotate_1.18.0     

 [7] xtable_1.5-2         AnnotationDbi_1.2.2  RSQLite_0.6-9       

[10] DBI_0.2-4            lattice_0.17-10      Biobase_2.0.1       

[13] limma_2.14.5        



thanks in advance for your advice

Zoe van Havre



Griffith University

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