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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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 ?crit 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 > >