Hello everyone,

 

I am doing beadsummary data analysis for illumina's WG-DASL data. I am using
beadarray package for analysis. Could anybody tell me why I am not getting

"QC Information" for my data as I am also importing qcFile.

Here is following script::

******************************************************

> library(beadarray)

> BSData  <-
readBeadSummaryData(dataFile="SampleProbeProfile.txt",qcFile="ControlProbePr
ofile.txt",sep="\t", skip=0, ProbeID="ProbeID",

+ columns = list(exprs ="AVG_Signal",se.exprs="BEAD_STDERR",nObservations =
"Avg_NBEADS", Detection="Detection Pval"),

+ qc.sep="\t",qc.skip=0, controlID="ProbeID",qc.columns =
list(exprs="AVG_Signal", se.exprs="BEAD_STDERR",

+ nObservations="Avg_NBEADS", Detection="Detection Pval"))

Warning message:

In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns,
:

  controlIDs non-unique: 4 repeated entries have been removed.

 

> BSData

ExpressionSetIllumina (storageMode: list)

assayData: 29785 features, 12 samples 

  element names: exprs, se.exprs, nObservations, Detection 

protocolData: none

phenoData

  rowNames: D1R_1 D2NR_1 ... Control_3 (12 total)

  varLabels: sampleID

  varMetadata: labelDescription

featureData

  featureNames: 6450255 2570615 ... 7650093 (29785 total)

  fvarLabels: ProbeID TargetID Status

  fvarMetadata: labelDescription

experimentData: use 'experimentData(object)'

Annotation:  

QC Information

Available Slots:  

  QC Items: 

  sampleNames: 

 

 

 

> sessionInfo()

R version 2.15.2 (2012-10-26)

Platform: x86_64-w64-mingw32/x64 (64-bit)

 

locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252

[4] LC_NUMERIC=C                           LC_TIME=English_United
States.1252    

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

 

other attached packages:

[1] beadarray_2.8.1    ggplot2_0.9.3.1    Biobase_2.18.0
BiocGenerics_0.4.0

 

loaded via a namespace (and not attached):

[1] AnnotationDbi_1.20.7 BeadDataPackR_1.10.0 colorspace_1.2-1     DBI_0.2-5
dichromat_2.0-0     

 [6] digest_0.6.3         grid_2.15.2          gtable_0.1.2
IRanges_1.16.6       labeling_0.2        

[11] limma_3.14.4         MASS_7.3-22          munsell_0.4
parallel_2.15.2      plyr_1.8            

[16] proto_0.3-10         RColorBrewer_1.0-5   reshape2_1.2.2
RSQLite_0.11.2       scales_0.2.3        

[21] stats4_2.15.2        stringr_0.6.2        tools_2.15.2        

******************************************************

 

Thanks,

Abdul Rawoof


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