[BioC] Chip version of Illumina HT 12 data [ lumi getChipInfo() method ]

[Mamunur Rashid]

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

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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!

########################################################################################



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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