[BioC] beadarray - can't load data

[Matt Ritchie]

Hi Zoe,

There are a few things you could look at.

1. Check the columns argument in readBeadSummaryData().  I think it should
be columns=list(exprs = "AVG_Signal",
                 NoBeads = "Avg_NBEADS",
                 Detection="Detection",
                 se.exprs="BEAD_STDEV")
rather than what you currently have.

2. If I've counted correctly, it looks as if you have 6 lines of header
information rather that 7.

3. Your sampleSheet is likely to cause problems - it looks like you are
specifying the file which contains probe information rather than a file
listing sample information about what was hybridised to each array.

Best wishes,

Matt

<Zoe.VanHavre at student.griffith.edu.au> wrote:

> 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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