[BioC] Constructing a LumiBatch manually

[Pan Du]

Hi Michal

I just checked the code and figured out the problem. The reason is that
Biobase made some changes recently, but I didn't modify my code accordingly.
Now I have fixed the problem in the lumi Release version (1.12.1) and
developing version (1.13.1). I may take several days before it is available.
Also you need to updated your R to 2.10.0 if you install the lumi package
using biocLite().
Thanks for reporting the problem.


Pan 


On 11/5/09 1:20 PM, "Gilbert Feng" <g-feng at northwestern.edu> wrote:

> From: Michal Blazejczyk <michal.blazejczyk at mail.mcgill.ca>
> Organization: Genome Quebec
> Reply-To: Michal Blazejczyk <michal.blazejczyk at mail.mcgill.ca>
> Date: Tue, 3 Nov 2009 12:15:39 -0500
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Constructing a LumiBatch manually
> 
> Dear group,
> 
> I have code that creates a LumiBatch object from two matrices of data:
> 
>   lumiBatch <- new( "LumiBatch", exprs = signalRaw, se.exprs = beadSD )
> 
> This code refuses to work in R 2.9:
> 
>   Error in `sampleNames<-`(`*tmp*`, value = character(0)) :
>     'value' length (0) must equal sample number in AssayData (0)
> 
> And I am unable to trace the source of the error.
> I've also tried setting up phenoData and featureData objects, to no avail.
> 
> FYI, the following call works fine:
>   lumiBatch <- new( "ExpressionSet", exprs = signalRaw, se.exprs = beadSD )
> 
> How can I fix this problem?
> 
> And this is my session info:
> 
> R version 2.9.2 (2009-08-24)
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETARY=Engl
> ish_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] lumi_1.10.2          RSQLite_0.7-2        DBI_0.2-4
> preprocessCore_1.6.0 mgcv_1.5-5           affy_1.22.1
> [7] annotate_1.22.0      AnnotationDbi_1.6.1  Biobase_2.4.1
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0   grid_2.9.2      lattice_0.17-25 nlme_3.1-93
> tools_2.9.2     xtable_1.5-5
> 
> Best,
> Michal