[BioC] new lumi and miRNA array data

[Cei Abreu-Goodger]

Hello Pan, et. al

I'm having some problems with a script that used to work before I upgraded 
to BioCondcutr 2.2 (and thus lumi 1.6.0).

Sorry I don't have an example for this, but maybe you can point me out in 
the right direction...

I get stuck when trying to run lumiT, this is what it looks like:

> raw <- lumiR(proFile, convertNuID=FALSE, inputAnnotation=FALSE)
> raw
Summary of BeadStudio output:
         Illumina Inc. BeadStudio version 3.2.6
         Normalization = none
         Array Content = mouseMI_V1_R0.bgx.xml
         Error Model = none
         DateTime = 03/03/2008 16:39
         Local Settings = en-GB

Major Operation History:
             submitted            finished
1 2008-05-05 19:41:48 2008-05-05 19:41:53
2 2008-05-05 19:41:53 2008-05-05 19:41:53
                                                          command 
lumiVersion
1 lumiR("Data/Sample_Gene_Profile.txt", inputAnnotation = FALSE) 
1.6.0
2              lumiQ(x.lumi = x.lumi, detectionTh = detectionTh) 
1.6.0

Object Information:
LumiBatch (storageMode: lockedEnvironment)
assayData: 386 features, 68 samples
   element names: beadNum, detection, exprs, se.exprs
phenoData
   sampleNames: Brain 1 wt_(well=A1_MAFID=1), Brain 2 wt_(well=B1_MAFID=2), 
...,
   Testes 3 KO_(well=H6_MAFID=48)  (68 total)
   varLabels and varMetadata description:
     sampleID: The unique Illumina microarray Id
featureData
   featureNames: mmu-let-7a, mmu-let-7b, ..., spike2-5240  (386 total)
   fvarLabels and fvarMetadata description:
     TargetID: The Illumina microarray identifier
experimentData: use 'experimentData(object)'
Annotation:
Control Data: Available
QC information: Please run summary(x, 'QC') for details!


> lumiVst <- lumiT(raw, method="vst")
2008-05-05 19:36:37 , processing array  1
2008-05-05 19:36:37 , processing array  2
...
2008-05-05 19:36:39 , processing array  67
2008-05-05 19:36:39 , processing array  68
There were 50 or more warnings (use warnings() to see the first 50)

> warnings()
Warning messages:
1: In lumiT(raw, method = "vst") ... :
   Too few probes are detectable based on detection p-values!
                          Iteration method will be used for VST.
2: In log(u.bak) ... : NaNs produced
...

==============

So, with lumi_1.4.0 I didn't get all these NaNs, now I do. Is this a 
feature? Any suggestions on how to deal with micro-RNA array data with the 
lumi package?

Many thanks,

Cei


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