Can't load annotations with lumi
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Steve Taylor ▴ 280
@steve-taylor-2838
Last seen 8.4 years ago
Hi, I am trying to analyse some Illumina data using lumi. I have installed 'lumiHumanAll.db' but when I try and read in the Illumina file it seems to load all the data except the annotation information... > x.lumi<-lumiR(fileName) Warning message: In addNuId2lumi(x.lumi, lib = lib) : Please provide the annotation file or lumi annotation library! If I include the name of the library... > x.lumi<-lumiR(fileName,lib="lumiHumanAll.db") Warning messages: 1: In addNuId2lumi(x.lumi, lib = lib) : lumiHumanAll.db does not include nuID conversion information! 2: In addNuId2lumi(x.lumi, lib = lib) : Please provide the annotation file or lumi annotation library! > x.lumi Summary of BeadStudio output: Illumina Inc. BeadStudio version 3.3.7 Normalization = none Array Content = HumanHT-12_V3_0_R1_11283641_A.bgx.xml Error Model = none DateTime = 18/11/2008 18:43 Local Settings = en-GB Major Operation History: submitted finished 1 2008-11-19 11:57:45 2008-11-19 11:57:57 2 2008-11-19 11:57:57 2008-11-19 11:58:00 command lumiVersion 1 lumiR("Sample_Probe_Profile.txt") 1.6.3 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh) 1.6.3 Object Information: LumiBatch (storageMode: lockedEnvironment) assayData: 48803 features, 24 samples element names: beadNum, detection, exprs, se.exprs phenoData sampleNames: AT1, AT2, ..., N12 (24 total) varLabels and varMetadata description: sampleID: The unique Illumina microarray Id featureData featureNames: 6450255, 2570615, ..., 4120753 (48803 total) fvarLabels and fvarMetadata description: ProbeID: The Illumina microarray identifier TargetID: The Illumina TargetID experimentData: use 'experimentData(object)' Annotation: Control Data: Available QC information: Please run summary(x, 'QC') for details! I am using R version 2.7.1 (2008-06-23). > packageDescription("lumi") Package: lumi Type: Package Title: BeadArray Specific Methods for Illumina Microarrays Version: 1.6.3 Date: 2008-09-17 Depends: R (>= 2.4.0), affy, mgcv (>= 1.4-0), methods Suggests: Biobase (>= 1.12.0), annotate, beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, genefilter, geneplotter, RColorBrewer Author: Pan Du, Warren Kibbe, Simon Lin Maintainer: Pan Du <dupan at="" northwestern.edu=""> Description: The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. License: LGPL version 2 or newer biocViews: Microarray, OneChannel, Preprocessing Packaged: Thu Sep 18 02:54:06 2008; biocbuild Built: R 2.7.1; ; 2008-11-19 11:38:36; unix My other question is (other than deleting the columns in the source files) if I QC an array and want to exclude it, how do I do that using the LumiBatch object? The data is exported from BeadStudio version 3.3.7. Thanks for any help, Steve ------------------------------------------------------------------ Medical Sciences Division Weatherall Institute of Molecular Medicine/Sir William Dunn School Oxford University
Microarray OneChannel Annotation Normalization probe Biobase annotate genefilter affy vsn • 1.2k views
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@kristen-k-dang-2922
Last seen 8.4 years ago
> Date: Wed, 19 Nov 2008 12:23:36 +0000 > From: Steve Taylor <stephen.taylor@imm.ox.ac.uk> > Subject: [BioC] Can't load annotations with lumi > To: Bioconductor <bioconductor@stat.math.ethz.ch> > Message-ID: <49240548.6070608@imm.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > I am trying to analyse some Illumina data using lumi. I have > installed 'lumiHumanAll.db' but when I try and read in the Illumina > file it seems to load all the data except the annotation information... > > > x.lumi<-lumiR(fileName) > Warning message: > In addNuId2lumi(x.lumi, lib = lib) : > Please provide the annotation file or lumi annotation library! > > If I include the name of the library... > > > x.lumi<-lumiR(fileName,lib="lumiHumanAll.db") > Warning messages: > 1: In addNuId2lumi(x.lumi, lib = lib) : > lumiHumanAll.db does not include nuID conversion information! > 2: In addNuId2lumi(x.lumi, lib = lib) : > Please provide the annotation file or lumi annotation library! > > > x.lumi > Summary of BeadStudio output: > Illumina Inc. BeadStudio version 3.3.7 > Normalization = none > Array Content = HumanHT-12_V3_0_R1_11283641_A.bgx.xml > Error Model = none > DateTime = 18/11/2008 18:43 > Local Settings = en-GB > > Major Operation History: > submitted finished > 1 2008-11-19 11:57:45 2008-11-19 11:57:57 > 2 2008-11-19 11:57:57 2008-11-19 11:58:00 > command lumiVersion > 1 lumiR("Sample_Probe_Profile.txt") 1.6.3 > 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh) 1.6.3 > > Object Information: > LumiBatch (storageMode: lockedEnvironment) > assayData: 48803 features, 24 samples > > My other question is (other than deleting the columns in the source > files) if I QC an array and want to exclude it, how do I do that > using the LumiBatch object? > > The data is exported from BeadStudio version 3.3.7. > > Thanks for any help, > > Steve > ------------------------------------------------------------------ > Medical Sciences Division > Weatherall Institute of Molecular Medicine/Sir William Dunn School > Oxford University > > Dear Steve, If what you are trying to accomplish is to get the NuID conversions to work properly, here is some sample code that I use that works. If I do otherwise, I get the errors you mentioned above. This code requires you to download the annotation file from the Illumina website and also to check that the column names in the BeadStudio export file are properly identified in the "annotationColName" specifier: input_file = "/path/to/your/BeadStudio/file" mydata.lumi = lumiR(input_file, inputAnnotation = FALSE) annotationFile = "../../annotation/HumanRef-8_V3_0_R1_11282963_A.txt" mydata.lumi = addNuId2lumi(x.lumi = mydata.lumi, annotationFile = annotationFile, annotationColName=c(sequence="Probe_Sequence", probe = "Probe_Id")) And for your other question, here is how to delete a sample from a LumiBatch object: Say you want to delete sample "A". First find where this sample is: which(sampleNames(mydata.lumi) == "A") Then delete it from the Lumi Object: mydata_reduced.lumi = mydata.lumi[,-30] where "30" is replaced by whatever response you get to the which(sampleNames) query. Hope that helps, Kristen Dang Postdoctoral Associate Duke Human Vaccine Institute www.duke.edu/~kd63 [[alternative HTML version deleted]]
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Pan Du ★ 1.2k
@pan-du-2010
Last seen 8.4 years ago
Hi Steve, Since lumi 1.8, we have two types of libraries. One is for ID mapping (mapping between Illumin IDs, nuIDs and RefSeq ID), which is named like lumiHumanIDMapping. Another is for annotation only, which is named like lumiHumanAll.db. So your command should be like: x.lumi<-lumiR(fileName,lib="lumiHumanIDMappng") Also please update your lumi to version 1.8.2 if it is not, and read the vignette "IlluminaAnnotation.pdf". Pan On 11/20/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Message: 1 > Date: Wed, 19 Nov 2008 12:23:36 +0000 > From: Steve Taylor <stephen.taylor at="" imm.ox.ac.uk=""> > Subject: [BioC] Can't load annotations with lumi > To: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <49240548.6070608 at imm.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > I am trying to analyse some Illumina data using lumi. I have installed > 'lumiHumanAll.db' but when I try and read in the Illumina file it seems to > load all the data except the annotation information... > >> x.lumi<-lumiR(fileName) > Warning message: > In addNuId2lumi(x.lumi, lib = lib) : > Please provide the annotation file or lumi annotation library! > > If I include the name of the library... > >> x.lumi<-lumiR(fileName,lib="lumiHumanAll.db") > Warning messages: > 1: In addNuId2lumi(x.lumi, lib = lib) : > lumiHumanAll.db does not include nuID conversion information! > 2: In addNuId2lumi(x.lumi, lib = lib) : > Please provide the annotation file or lumi annotation library! > >> x.lumi > Summary of BeadStudio output: > Illumina Inc. BeadStudio version 3.3.7 > Normalization = none > Array Content = HumanHT-12_V3_0_R1_11283641_A.bgx.xml > Error Model = none > DateTime = 18/11/2008 18:43 > Local Settings = en-GB > > Major Operation History: > submitted finished > 1 2008-11-19 11:57:45 2008-11-19 11:57:57 > 2 2008-11-19 11:57:57 2008-11-19 11:58:00 > command lumiVersion > 1 lumiR("Sample_Probe_Profile.txt") 1.6.3 > 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh) 1.6.3 > > Object Information: > LumiBatch (storageMode: lockedEnvironment) > assayData: 48803 features, 24 samples > element names: beadNum, detection, exprs, se.exprs > phenoData > sampleNames: AT1, AT2, ..., N12 (24 total) > varLabels and varMetadata description: > sampleID: The unique Illumina microarray Id > featureData > featureNames: 6450255, 2570615, ..., 4120753 (48803 total) > fvarLabels and fvarMetadata description: > ProbeID: The Illumina microarray identifier > TargetID: The Illumina TargetID > experimentData: use 'experimentData(object)' > Annotation: > Control Data: Available > QC information: Please run summary(x, 'QC') for details! > > I am using R version 2.7.1 (2008-06-23). > >> packageDescription("lumi") > Package: lumi > Type: Package > Title: BeadArray Specific Methods for Illumina Microarrays > Version: 1.6.3 > Date: 2008-09-17 > Depends: R (>= 2.4.0), affy, mgcv (>= 1.4-0), methods > Suggests: Biobase (>= 1.12.0), annotate, beadarray, limma, vsn, > lumiBarnes, lumiHumanAll.db, genefilter, geneplotter, > RColorBrewer > Author: Pan Du, Warren Kibbe, Simon Lin > Maintainer: Pan Du <dupan at="" northwestern.edu=""> > Description: The lumi package provides an integrated solution for the > Illumina microarray data analysis. It includes functions of > Illumina BeadStudio data input, quality control, > BeadArray-specific variance stabilization, normalization and > gene annotation at the probe level. > License: LGPL version 2 or newer > biocViews: Microarray, OneChannel, Preprocessing > Packaged: Thu Sep 18 02:54:06 2008; biocbuild > Built: R 2.7.1; ; 2008-11-19 11:38:36; unix > > My other question is (other than deleting the columns in the source files) if > I QC an array and want to exclude it, how do I do that using the LumiBatch > object? > > The data is exported from BeadStudio version 3.3.7. > > Thanks for any help, > > Steve > ------------------------------------------------------------------ > Medical Sciences Division > Weatherall Institute of Molecular Medicine/Sir William Dunn School > Oxford University
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