[BioC] problem with createBeadSummaryData

[Mark Dunning]

Hi Philip,

The key to this problem is to set the 'imagesPerArray'  argument. This
dataset is quite an old one ("Humanv1") and back then Illumina used to
put different probes on the two stripes (e.g A_1 and A_2) for each
sample. Running createBeadSummaryData with the default option of
imagesPerArray =1 will confuse beadarray in this case as it will
expect to find the same probes on A_1 and A_2, and will produce NA
values when it doesn't.

The following command should be used for this dataset:-

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

More modern Illumina data (v2 and v3) have the same set of probes on
both stripes so the default arguments should work.

Regards,

Mark

On Thu, Mar 5, 2009 at 3:04 PM, Groot, Philip de <philip.degroot at wur.nl> wrote:
> 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)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> 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
>>
>
> Regards,
>
> 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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