[BioC] Problems with VST in lumi

[Michal Blazejczyk]

Hi,

We are creating lumiBatch objects manually the following way, using matrices
of data:

 if( !exists( "controlData" ) )  controlData <- data.frame()
 if( !use.beadCounts )  beadCount <- new( "matrix" )  # otherwise the object already exists
 if( !use.detPValues )  detectionPValue <- new( "matrix" )  # otherwise the object already exists

 lumiBatch <- new( "LumiBatch", exprs = signalRaw, se.exprs = beadSD,
                   featureData = featureData, phenoData = phenoData,
                   controlData = controlData,
                   beadNum = beadCount, detection = detectionPValue )

 lumiBatch <- lumiQ( lumiBatch )

 results <- lumiExpresso( lumiBatch, verbose = TRUE,
                          bg.correct = FALSE,
                          bgcorrect.param = list( method = "none" ),
                          variance.stabilize = TRUE,
                          varianceStabilize.param = list( method = "vst" ),
                          normalize = FALSE,
                          normalize.param = list( method = "none" ),
                          QC.evaluation = FALSE )

When I run this, I get the following error:

  Variance Stabilizing Transform method: vst
  Variance stabilizing ...
  Perform vst transformation ...
  No Standard Deviation correction was applied becasue of missing bead number information.
  Error in !assayDataValidMembers(assayData(x.lumi), "detection") :
    invalid argument type

I assume that one of the functions called by lumiExpresso() is looking for the detection
slot of the lumiBatch, but does not find it or finds it to be of the wrong type.

BTW, the same error happens if I *don't* specify the detection parameter when creating
the lumiBatch...

How, then, should I specify "detection" in the call to new("LumiBatch",...)
when detection p-values are not available and if I want to use lumi?

> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C                    LC_TIME=English_Canada.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lumi_2.2.1     Biobase_2.10.0

Best regards,

Michał Błażejczyk
FlexArray Lead Developer
McGill University and Genome Quebec Innovation Centre
http://www.gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e