[BioC] LumiBatch - Error in creating lumi object

Pan Du dupan at northwestern.edu
Wed Aug 27 17:25:09 CEST 2008


Hi Sharon,

You should make each element of AssayData slot have the same row names and
column names. Here is an example of creating new LumiBatch object. The exprs
and se.exprs are required, others are optional.

 library(lumi)
 data(example.lumi)
 newLumi = new('LumiBatch', exprs=exprs(example.lumi),
se.exprs=se.exprs(example.lumi), detection=detection(example.lumi),
beadNum=beadNum(example.lumi))


Pan



On 8/27/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 6
> Date: Tue, 26 Aug 2008 16:38:13 +0100
> From: Sharon <sharonanandhi at gmail.com>
> Subject: [BioC] LumiBatch - Error in creating lumi object
> To: bioconductor at stat.math.ethz.ch
> Message-ID:
> <3709c2370808260838s59061dc7kcdc46908b9139fe2 at mail.gmail.com>
> Content-Type: text/plain
> 
> Hi,
> 
> Since my datafile is not in a standard format, I am trying to create a new
> lumi object with following information: AVG_Signal, Detection.Pval,
> Avg_NBEADS and BEAD_STDERR. I have used,
> 
> require(lumi)
> dat.lumi <- new('LumiBatch', exprs = as.matrix(signalRaw), se.exprs =
> as.matrix(std), beadNum = as.matrix(nb), detection = as.matrix(detP) )
> 
> I am getting:
> 
> Error in validObject(.Object) :
>   invalid class "LumiBatch" object: sampleNames differ between assayData and
> phenoData
> 
>> sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> base
> 
> other attached packages:
> [1] lumi_1.6.2           mgcv_1.4-0           affy_1.18.2
> preprocessCore_1.2.1 affyio_1.8.1         Biobase_2.0.1
> 
> Am I doing anything wrong?
> 
> Thanks in advance.
> 
> Best regards,
> Sharon
> 
> [[alternative HTML version deleted]]
> 
>



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