[BioC] problem with createBeadSummaryData

Groot, Philip de philip.degroot at wur.nl
Thu Mar 5 16:04:37 CET 2009

Hello all,
I encountered a problem with the createBeadSummaryData function in the beadarray library.
I use the Illumina example files that are available on: http://www.compbio.group.cam.ac.uk/Resources/illumina/BeadLevelExample.zip

I use the readIllimuna() command to read the files into Bioconductor:

readIllumina(arrayNames = Illumina_Files_Listed, textType=".csv", useImages=F, backgroundMethod="none", singleChannel=TRUE)

When I try to summarize the BeadLevel object, this works:

x.norm <- createBeadSummaryData(x.illumina, log=FALSE, what="G", method="illumina")

However, I obtain weird exprs-values:

> exprs(x)[1:5,]
      1475542113_A_1 1475542113_A_2 1475542113_B_1 1475542113_B_2
50008       821.4375            NaN       854.6316            NaN
50014      4154.5500            NaN      3782.0000            NaN
50017     21880.9574            NaN     21404.0909            NaN
50020       110.8542            NaN       116.9821            NaN
50022       129.4857            NaN       107.9600            NaN

every 2nd column is completely NaN although I correctly state that only the green channels should be used. Is this a bug in the createBeadSummaryData function?

If I do the summarization array by array, it does make more sense:

x.norm.2 <- createBeadSummaryData(x.illumina, log=FALSE, what="G", method="illumina", arrays=2)

> exprs(x.norm.2)[1:5]
[1] 869.3913 112.5909 104.4375 116.5116 125.0000
> arrayNames(x.illumina)[2]
[1] "1475542113_A_2"

So: what causes this particular behaviour? Do I misunderstand something? What is the best way to get the summarization properly done? My goal is to create an ExpressionSetIllumina object on which I can perform normalization (quantile, vsn, etc.).

> sessionInfo()
R version 2.8.0 (2008-10-20)


attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] vsn_3.8.0           affy_1.20.0         beadarray_1.10.0
 [4] sma_0.5.15          hwriter_1.0         geneplotter_1.20.0
 [7] annotate_1.20.1     xtable_1.5-4        AnnotationDbi_1.4.2
[10] lattice_0.17-20     Biobase_2.2.1       limma_2.16.3

loaded via a namespace (and not attached):
[1] affyio_1.10.1        DBI_0.2-4            grid_2.8.0
[4] KernSmooth_2.22-22   marray_1.20.0        preprocessCore_1.4.0
[7] RColorBrewer_1.0-2   RSQLite_0.7-1        tcltk_2.8.0


Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl> 
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/> 

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