[BioC] new lumi and miRNA array data

[Wolfgang Huber]

Dear Cei,

I think it would be helpful for resolving this to make available to the 
lumi maintainers (and to this list) a reproducible example, including 
your (anonymized and/or reduced) dataset.

	Best wishes
	Wolfgang



------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

Cei Abreu-Goodger a écrit 05/05/2008 19:51:
> 
> 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
> 
>