[BioC] beadarray observation (nObservations actually) regarding number of beads in Red vs. Grn channels

[Mark Dunning]

Hi Tim,

Many thanks for your comments on the new beadarray. We have indeed
made many changes that we hope will help users with Illumina data
other than expression.

The nObservations matrix is constructed after summarisation and the
removal of outliers. When you specify more than one channel in
'summarize', outlier removal is done separately on each channel. It is
possible that different beads could get removed in the different
channels and therefore the numbers in nObservations would be
different.

Mark



On Mon, Nov 1, 2010 at 8:53 AM, Tim Triche <tim.triche at gmail.com> wrote:
> I randomly sucked in a bunch of old HumanMethylation27k files into the shiny
> new beadarray package (which is great, by the way) and saw:
>
>> summary(nObservations(bsd)[,1] - nObservations(bsd)[,13])
>     Min.   1st Qu.    Median      Mean   3rd Qu.      Max.
> -6.000000  0.000000  0.000000 -0.004919  0.000000  8.000000
>
>> colnames(nObservations(bsd))[c(1,13)]
> [1] "Grn:5543338058_A" "Red:5543338058_A"
>
> That seems odd -- aren't there supposed to be the same number of beads in
> the red channel as the green (they're all just scanned twice, rite)?
>
> I figured I'd read in a bunch of 27k chips before going to town on the 450k
> chips, which currently only give me .idat files to crack open.  The other
> irritating little niggles should provide endless entertainment, but the
> newer chips seem to at least have vastly superior control probes.
>
> Great, great, great revision to the data structures and overall package.
>  It's really quite usable now for methylation arrays.
>
> Almost forgot:
>
>> sessionInfo()
> R version 2.13.0 Under development (unstable) (2010-10-15 r53334)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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 datasets  utils     methods   base
>
> other attached packages:
> [1] methylumiCSV_1.12 matrixStats_0.2.2 R.methodsS3_1.2.1 methylumi_1.5.0
> [5] beadarray_2.1.1   Biobase_2.11.2    plyr_1.2.1        reshape2_1.0
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.0     lattice_0.19-13 limma_3.7.8     stringr_0.4
> [5] tools_2.13.0
>
> --
> If people do not believe that mathematics is simple, it is only because they
> do not realize how complicated life is.
> John von Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>
>
>        [[alternative HTML version deleted]]
>
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