[BioC] Changes in lumi in 2.9.2?

Michal Blazejczyk michal.blazejczyk at mail.mcgill.ca
Wed Sep 30 17:50:33 CEST 2009


We have custom code that creates LumiBatch objects from data.
First, we create an AnnotatedDataFrame for both phenoData and
featureData.  Then we create the LumiBatch this way:

    lumiBatch <- new( "LumiBatch", exprs = signalRaw, se.exprs = beadSD,
        featureData = featureData, phenoData = phenoData )

In R 2.9.2 we are getting the following error message:

  error in sample names<= tmp value = c (sample 1 sample 2 sample 3)
    value length (8) must equal sample number in assay data (0).

I have a question for lumi developers, were there changes in the most
recent version of the lumi package that would make such code stop

I can send the entire script, but I thought that maybe it isn't
necessary (in the case when this is a known change in behavior).

Here's the sessionInfo():

R version 2.9.2 (2009-08-24)


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           
[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    
[5] tools_2.9.2     xtable_1.5-5


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