Hi Alison,

I guess the data you have does not include the ³BEAD_STDERR² columns, which
are required to create LumiBatch object. lumiR will create an ExpressionSet
object if the ³BEAD_STDERR² columns are not available in the file.

Ask your core facility to output ³AVG_Signal², ³BEAD_STDERR², ³Detection
Pval² columns, probably also ³Avg_NBEADS². If there are not many samples, I
recommend output all columns BeadStudio can output.


Pan


On 7/31/08 1:54 PM, "Alison Ziesel" <aziesel@emory.edu> wrote:

> Dear Dr. Du,
> 
> I am a graduate student, currently learning to analyze microarray data both
> for my own research and for some of our laboratory's collaborations. I've
> recently been given data from an Illumina array experiment to analyze, and
> would like very much to do so using your lumi package. However, I've been
> having difficulties importing the data files provided by our microarray
> facility, and suspect that I am either using incomplete or incorrectly
> formatted BeadStudio data. When I am able  to import data using lumiR, I am
> unable to create a lumiBatch object; rather, I get a generic ExpressionSet
> object, which if I understand correctly, cannot take full advantage of the
> lumi package for subsequent analysis.
> 
> Here is the sequence of commands I've used to get this far:
> 
>> > library("lumi")
>> > library("lumiRatV1")
>> > test_read <- lumiR("SampleProbeSignal.txt", lib = "lumiRatV1")
>> > test_read
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 22523 features, 21 samples 
>   element names: exprs 
> phenoData
>   sampleNames: 76-PW-1, 76-PW-1a, ..., 76-PW-7b  (21 total)
>   varLabels and varMetadata description:
>     sampleID: The unique Illumina microarray Id
>     label: The label of the sample
> featureData
>   featureNames: ILMN_1369537, ILMN_1358051, ..., ILMN_1352673  (22523 total)
>   fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation:
> 
> 
> And here is my session info:
> 
>> > sessionInfo()
> R version 2.6.2 (2008-02-08) 
> powerpc-apple-darwin8.10.1 
> 
> locale:
> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods   base
>     
> 
> other attached packages:
>  [1] lumiRatV1_1.3.1      lumi_1.4.0           annotate_1.16.1    
>  xtable_1.5-2        
>  [5] AnnotationDbi_1.0.6  RSQLite_0.6-8        DBI_0.2-4          
>  mgcv_1.3-29         
>  [9] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1        
> Biobase_1.16.3      
> 
> 
> I am not sure if attaching my SampleProbeSignal.txt file will be useful to you
> or not. Essentially, what I hope to learn from you is the exact format of file
> to request from our microarray facility staff, so that I can proceed with the
> lumi package from there. If there is any further information required
> regarding my problem I will be happy to provide it. I am very grateful for any
> assistance you may be able to provide, and look forward to hearing from you.
> 
> 
>  
> Alison Ziesel
> Department of Ophthalmology, Emory University
> aziesel@emory.edu
> 
> 
 



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