[BioC] Changes in lumi in 2.9.2?
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:
 stats graphics grDevices utils datasets methods base
other attached packages:
 lumi_1.10.2 RSQLite_0.7-2 DBI_0.2-4
 preprocessCore_1.6.0 mgcv_1.5-5 affy_1.22.1
 annotate_1.22.0 AnnotationDbi_1.6.1 Biobase_2.4.1
loaded via a namespace (and not attached):
 affyio_1.12.0 grid_2.9.2 lattice_0.17-25 nlme_3.1-93
 tools_2.9.2 xtable_1.5-5
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