[BioC] beadarray package: problem with object made by createBeadSummaryData
Matt Ritchie
Matt.Ritchie at cancer.org.uk
Mon Nov 12 20:00:44 CET 2007
Hi Krys,
This is a bug, which has been fixed in beadarray 1.7.2. Thanks for pointing
it out! Best wishes,
Matt
> Hello
>
> Using R 2.5.1, I have read in and explored the bead level data from 5
> Illumina mouse-6 slides which have 6 arrays per slide and 2 images per
> array.
>
> I have also created and saved bead summary data trying out a few options for
> the background correction.
>
> When I was using R 2.5.1 and the corresponding versions of bioconductor and
> beadarray and everything worked fine.
>
> But I want to upgrade to R 2.6.0. I have installed R 2.6.0 and the
> corresponding versions of bioconductor and beadarray. I now find that
> se.exprs is completely filled with NAs.
>
> I have compared the documentation from the two versions of beadarray
> expecting that there was a new option that I needed to specify, but I can't
> find anything that would account for the NAs
>
> Please can you suggest what the problem is.
>
> My program code, output from the BSData object and sessionInfo() are pasted
> below.
>
> Thanks
>
> Krys
>
>
> PROGRAM CODE
> ------------
> # Read the bead level data
> BLData39A <- readIllumina(arrayNames=c("1863191039_A_1", "1863191039_A_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData39B <- readIllumina(arrayNames=c("1863191039_B_1", "1863191039_B_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData39C <- readIllumina(arrayNames=c("1863191039_C_1", "1863191039_C_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData39D <- readIllumina(arrayNames=c("1863191039_D_1", "1863191039_D_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData39E <- readIllumina(arrayNames=c("1863191039_E_1", "1863191039_E_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData39F <- readIllumina(arrayNames=c("1863191039_F_1", "1863191039_F_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
>
> BLData46A <- readIllumina(arrayNames=c("1863191046_A_1", "1863191046_A_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData46B <- readIllumina(arrayNames=c("1863191046_B_1", "1863191046_B_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData46C <- readIllumina(arrayNames=c("1863191046_C_1", "1863191046_C_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData46D <- readIllumina(arrayNames=c("1863191046_D_1", "1863191046_D_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData46E <- readIllumina(arrayNames=c("1863191046_E_1", "1863191046_E_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData46F <- readIllumina(arrayNames=c("1863191046_F_1", "1863191046_F_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
>
> BLData49A <- readIllumina(arrayNames=c("1863191049_A_1", "1863191049_A_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData49B <- readIllumina(arrayNames=c("1863191049_B_1", "1863191049_B_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData49C <- readIllumina(arrayNames=c("1863191049_C_1", "1863191049_C_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData49D <- readIllumina(arrayNames=c("1863191049_D_1", "1863191049_D_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData49E <- readIllumina(arrayNames=c("1863191049_E_1", "1863191049_E_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData49F <- readIllumina(arrayNames=c("1863191049_F_1", "1863191049_F_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
>
> BLData50A <- readIllumina(arrayNames=c("1863191050_A_1", "1863191050_A_2"),
> textType=".txt", backgroundMethod="none", rmoffset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData50B <- readIllumina(arrayNames=c("1863191050_B_1", "1863191050_B_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData50C <- readIllumina(arrayNames=c("1863191050_C_1", "1863191050_C_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData50D <- readIllumina(arrayNames=c("1863191050_D_1", "1863191050_D_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData50E <- readIllumina(arrayNames=c("1863191050_E_1", "1863191050_E_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData50F <- readIllumina(arrayNames=c("1863191050_F_1", "1863191050_F_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
>
> BLData52A <- readIllumina(arrayNames=c("1863191052_A_1", "1863191052_A_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData52B <- readIllumina(arrayNames=c("1863191052_B_1", "1863191052_B_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData52C <- readIllumina(arrayNames=c("1863191052_C_1", "1863191052_C_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData52D <- readIllumina(arrayNames=c("1863191052_D_1", "1863191052_D_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData52E <- readIllumina(arrayNames=c("1863191052_E_1", "1863191052_E_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
> BLData52F <- readIllumina(arrayNames=c("1863191052_F_1", "1863191052_F_2"),
> textType=".txt", backgroundMethod="none", offset=0,normalizeMethod="none",
> metrics=FALSE)
>
> # Creation of summary data
> BSData39A <- createBeadSummaryData(BLData39A, log=FALSE,n=3,
> imagesPerArray=2)
> BSData39B <- createBeadSummaryData(BLData39B, log=FALSE,n=3,
> imagesPerArray=2)
> BSData39C <- createBeadSummaryData(BLData39C, log=FALSE,n=3,
> imagesPerArray=2)
> BSData39D <- createBeadSummaryData(BLData39D, log=FALSE,n=3,
> imagesPerArray=2)
> BSData39E <- createBeadSummaryData(BLData39E, log=FALSE,n=3,
> imagesPerArray=2)
> BSData39F <- createBeadSummaryData(BLData39F, log=FALSE,n=3,
> imagesPerArray=2)
>
> BSData46A <- createBeadSummaryData(BLData46A, log=FALSE,n=3,
> imagesPerArray=2)
> BSData46B <- createBeadSummaryData(BLData46B, log=FALSE,n=3,
> imagesPerArray=2)
> BSData46C <- createBeadSummaryData(BLData46C, log=FALSE,n=3,
> imagesPerArray=2)
> BSData46D <- createBeadSummaryData(BLData46D, log=FALSE,n=3,
> imagesPerArray=2)
> BSData46E <- createBeadSummaryData(BLData46E, log=FALSE,n=3,
> imagesPerArray=2)
> BSData46F <- createBeadSummaryData(BLData46F, log=FALSE,n=3,
> imagesPerArray=2)
>
> BSData49A <- createBeadSummaryData(BLData49A, log=FALSE,n=3,
> imagesPerArray=2)
> BSData49B <- createBeadSummaryData(BLData49B, log=FALSE,n=3,
> imagesPerArray=2)
> BSData49C <- createBeadSummaryData(BLData49C, log=FALSE,n=3,
> imagesPerArray=2)
> BSData49D <- createBeadSummaryData(BLData49D, log=FALSE,n=3,
> imagesPerArray=2)
> BSData49E <- createBeadSummaryData(BLData49E, log=FALSE,n=3,
> imagesPerArray=2)
> BSData49F <- createBeadSummaryData(BLData49F, log=FALSE,n=3,
> imagesPerArray=2)
>
> BSData50A <- createBeadSummaryData(BLData50A, log=FALSE,n=3,
> imagesPerArray=2)
> BSData50B <- createBeadSummaryData(BLData50B, log=FALSE,n=3,
> imagesPerArray=2)
> BSData50C <- createBeadSummaryData(BLData50C, log=FALSE,n=3,
> imagesPerArray=2)
> BSData50D <- createBeadSummaryData(BLData50D, log=FALSE,n=3,
> imagesPerArray=2)
> BSData50E <- createBeadSummaryData(BLData50E, log=FALSE,n=3,
> imagesPerArray=2)
> BSData50F <- createBeadSummaryData(BLData50F, log=FALSE,n=3,
> imagesPerArray=2)
>
> BSData52A <- createBeadSummaryData(BLData52A, log=FALSE,n=3,
> imagesPerArray=2)
> BSData52B <- createBeadSummaryData(BLData52B, log=FALSE,n=3,
> imagesPerArray=2)
> BSData52C <- createBeadSummaryData(BLData52C, log=FALSE,n=3,
> imagesPerArray=2)
> BSData52D <- createBeadSummaryData(BLData52D, log=FALSE,n=3,
> imagesPerArray=2)
> BSData52E <- createBeadSummaryData(BLData52E, log=FALSE,n=3,
> imagesPerArray=2)
> BSData52F <- createBeadSummaryData(BLData52F, log=FALSE,n=3,
> imagesPerArray=2)
>
> BSData <- combine(
> BSData39A, BSData39B, BSData39C, BSData39D, BSData39E, BSData39F,
> BSData46A, BSData46B, BSData46C, BSData46D, BSData46E, BSData46F,
> BSData49A, BSData49B, BSData49C, BSData49D, BSData49E, BSData49F,
> BSData50A, BSData50B, BSData50C, BSData50D, BSData50E, BSData50F,
> BSData52A, BSData52B, BSData52C, BSData52D, BSData52E, BSData52F)
>
>
> OUTPUT FROM SESSSION USING BSData
> ---------------------------------
>
>> BSData
> ExpressionSetIllumina (storageMode: list)
> assayData: 48358 features, 30 samples
> element names: exprs, se.exprs, NoBeads
> phenoData
> rowNames: 1863191039_A_1, 1863191039_B_1, ..., 1863191052_F_1 (30 total)
> varLabels and varMetadata description:
> arrayName: NA
> featureData
> featureNames:
> fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation: illuminaProbeIDs
>> slotNames(BSData)
> [1] "QC" "assayData" "phenoData"
> [4] "featureData" "experimentData" "annotation"
> [7] ".__classVersion__"
>> names(assayData(BSData))
> [1] "exprs" "se.exprs" "NoBeads"
>> dim(assayData(BSData)$exprs)
> [1] 48358 30
>> dim(assayData(BSData)$se.exprs)
> [1] 48358 30
>> exprs(BSData)[1:10,1:2]
> 1863191039_A_1 1863191039_B_1
> 10243 84.31794 90.07728
> 10280 77.86524 78.17629
> 10575 148.53714 154.93587
> 20048 74.88917 71.63645
> 20296 18520.55707 20620.06535
> 20343 60.40684 61.49921
> 20373 64.48009 63.93970
> 20431 26997.07647 29130.48258
> 50008 114.36110 267.88378
> 50014 47.48685 43.68849
>> se.exprs(BSData)[1:10,1:2]
> 1863191039_A_1 1863191039_B_1
> 10243 NA NA
> 10280 NA NA
> 10575 NA NA
> 20048 NA NA
> 20296 NA NA
> 20343 NA NA
> 20373 NA NA
> 20431 NA NA
> 50008 NA NA
> 50014 NA NA
>> pData(BSData)[,1]
> 1863191039_A_1 1863191039_B_1 1863191039_C_1 1863191039_D_1 1863191039_E_1
> 1863191039_A_1 1863191039_B_1 1863191039_C_1 1863191039_D_1 1863191039_E_1
> 1863191039_F_1 1863191046_A_1 1863191046_B_1 1863191046_C_1 1863191046_D_1
> 1863191039_F_1 1863191046_A_1 1863191046_B_1 1863191046_C_1 1863191046_D_1
> 1863191046_E_1 1863191046_F_1 1863191049_A_1 1863191049_B_1 1863191049_C_1
> 1863191046_E_1 1863191046_F_1 1863191049_A_1 1863191049_B_1 1863191049_C_1
> 1863191049_D_1 1863191049_E_1 1863191049_F_1 1863191050_A_1 1863191050_B_1
> 1863191049_D_1 1863191049_E_1 1863191049_F_1 1863191050_A_1 1863191050_B_1
> 1863191050_C_1 1863191050_D_1 1863191050_E_1 1863191050_F_1 1863191052_A_1
> 1863191050_C_1 1863191050_D_1 1863191050_E_1 1863191050_F_1 1863191052_A_1
> 1863191052_B_1 1863191052_C_1 1863191052_D_1 1863191052_E_1 1863191052_F_1
> 1863191052_B_1 1863191052_C_1 1863191052_D_1 1863191052_E_1 1863191052_F_1
> 30 Levels: 1863191039_A_1 1863191039_B_1 1863191039_C_1 ... 1863191052_F_1
>> pData(BSData)[,2]
> NULL
>> pData(BSData)[,2]
> NULL
>> pData(BSData)[,1]
> 1863191039_A_1 1863191039_B_1 1863191039_C_1 1863191039_D_1 1863191039_E_1
> 1863191039_F_1 1863191046_A_1
> 1863191039_A_1 1863191039_B_1 1863191039_C_1 1863191039_D_1 1863191039_E_1
> 1863191039_F_1 1863191046_A_1
> 1863191046_B_1 1863191046_C_1 1863191046_D_1 1863191046_E_1 1863191046_F_1
> 1863191049_A_1 1863191049_B_1
> 1863191046_B_1 1863191046_C_1 1863191046_D_1 1863191046_E_1 1863191046_F_1
> 1863191049_A_1 1863191049_B_1
> 1863191049_C_1 1863191049_D_1 1863191049_E_1 1863191049_F_1 1863191050_A_1
> 1863191050_B_1 1863191050_C_1
> 1863191049_C_1 1863191049_D_1 1863191049_E_1 1863191049_F_1 1863191050_A_1
> 1863191050_B_1 1863191050_C_1
> 1863191050_D_1 1863191050_E_1 1863191050_F_1 1863191052_A_1 1863191052_B_1
> 1863191052_C_1 1863191052_D_1
> 1863191050_D_1 1863191050_E_1 1863191050_F_1 1863191052_A_1 1863191052_B_1
> 1863191052_C_1 1863191052_D_1
> 1863191052_E_1 1863191052_F_1
> 1863191052_E_1 1863191052_F_1
> 30 Levels: 1863191039_A_1 1863191039_B_1 1863191039_C_1 1863191039_D_1
> 1863191039_E_1 ... 1863191052_F_1
>> pData(BSData)[,1]
> 1863191039_A_1 1863191039_B_1 1863191039_C_1 1863191039_D_1 1863191039_E_1
> 1863191039_F_1
> 1863191039_A_1 1863191039_B_1 1863191039_C_1 1863191039_D_1 1863191039_E_1
> 1863191039_F_1
> 1863191046_A_1 1863191046_B_1 1863191046_C_1 1863191046_D_1 1863191046_E_1
> 1863191046_F_1
> 1863191046_A_1 1863191046_B_1 1863191046_C_1 1863191046_D_1 1863191046_E_1
> 1863191046_F_1
> 1863191049_A_1 1863191049_B_1 1863191049_C_1 1863191049_D_1 1863191049_E_1
> 1863191049_F_1
> 1863191049_A_1 1863191049_B_1 1863191049_C_1 1863191049_D_1 1863191049_E_1
> 1863191049_F_1
> 1863191050_A_1 1863191050_B_1 1863191050_C_1 1863191050_D_1 1863191050_E_1
> 1863191050_F_1
> 1863191050_A_1 1863191050_B_1 1863191050_C_1 1863191050_D_1 1863191050_E_1
> 1863191050_F_1
> 1863191052_A_1 1863191052_B_1 1863191052_C_1 1863191052_D_1 1863191052_E_1
> 1863191052_F_1
> 1863191052_A_1 1863191052_B_1 1863191052_C_1 1863191052_D_1 1863191052_E_1
> 1863191052_F_1
> 30 Levels: 1863191039_A_1 1863191039_B_1 1863191039_C_1 1863191039_D_1 ...
> 1863191052_F_1
>>
>>
>
> SESSION INFO
> ------------
>> sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] tools stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] beadarray_1.6.0 affy_1.16.0 preprocessCore_1.0.0
> affyio_1.6.1
> [5] geneplotter_1.16.0 lattice_0.16-5 annotate_1.16.1
> xtable_1.5-2
> [9] AnnotationDbi_1.0.6 RSQLite_0.6-4 DBI_0.2-4
> Biobase_1.16.1
> [13] limma_2.12.0
>
> loaded via a namespace (and not attached):
> [1] grid_2.6.0 KernSmooth_2.22-21 RColorBrewer_1.0-2
>>
>>
>>
>> pData(BSData)[1,1]
> 1863191039_A_1
> 1863191039_A_1
> 30 Levels: 1863191039_A_1 1863191039_B_1 1863191039_C_1 1863191039_D_1 ...
> 1863191052_F_1
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