Question: Chip version of Illumina HT 12 data [ lumi getChipInfo() method ]
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gravatar for Md.Mamunur Rashid
8.1 years ago by
Md.Mamunur Rashid260 wrote:
Dear List, I am working on some Illumina-HT12 data. There seems to be a small problem in using the getChipInfo() method in lumi package. Thought the data is from Illumina HT-12 chip, the getchipInfo() returns "HumanWG6_V2_11223189_B" as chip version. Any information or suggestion regarding this issue will be really appreciated. regards, Mamun ################################################## Here is the LumiBatch object details. Data_New_Read Summary of data information: Data File Information: Illumina Inc. BeadStudio version 3.4.0 Normalization = none Array Content = HumanHT-12_V3_0_R1_11283641_A.bgx.xml Error Model = none DateTime = 11/12/2009 17:04 Local Settings = fr-FR Major Operation History: submitted finished 1 2011-05-25 16:01:01 2011-05-25 16:03:09 2 2011-05-25 16:03:09 2011-05-25 16:03:27 command 1 lumiR("/media/Win7-64/ANEU_FV_Sample_Probe_Profile.txt") 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) lumiVersion 1 1.14.0 2 1.14.0 Object Information: LumiBatch (storageMode: lockedEnvironment) assayData: 48803 features, 288 samples element names: beadNum, detection, exprs, se.exprs protocolData: none phenoData sampleNames: 4968529003_A, 4968529003_B, ..., 4856050028_L (288 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! ###################################################################### ################## ################################################### SessionInfo : sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumiHumanAll.db_1.10.1 lumiHumanIDMapping_1.6.2 [3] illuminaHumanv3BeadID.db_1.6.0 org.Hs.eg.db_2.4.1 [5] lumi_1.14.0 MASS_7.3-6 [7] RSQLite_0.9-1 DBI_0.2-5 [9] preprocessCore_1.10.0 mgcv_1.6-2 [11] affy_1.26.1 annotate_1.26.0 [13] AnnotationDbi_1.10.1 Biobase_2.8.0 [15] session_1.0.2 samr_1.28 [17] impute_1.22.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 grid_2.11.1 lattice_0.18-8 Matrix_0.999375-39 [5] nlme_3.1-96 tools_2.11.1 xtable_1.5-6 ###################################################################### ######### -- Md.Mamunur Rashid Breakthrough Breast Cancer Research Unit Research Oncology Kings College London 3rd Floor Bermondsey Wing Guy's Hospital Great Maze Pond London, SE1 9RT Tel: 020 7188 7188 ext.51093 Fax: 020 7188 3666
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