Entering edit mode
Hi Keith -- I'll let Mark make changes to his package, but actually a
quick peak at the documentation for assayDataNew (e.g.,
help("assayDataNew")) shows that the argument should be 'storage.mode'
rather than storageMode.
By default, assayDataNew returns an 'environment', which is what you
see with your first example. You can see the contents of an
environment with the 'ls()' command (this is analogous to 'names()'
applied to lists), and can access individual members of the
environment
with '$' or '[[' (you cannot subset an environment with '[',
though).
Probably the data is there and usable, just not in the form expected.
Hope that helps,
Martin
Keith Satterley <keith at="" wehi.edu.au=""> writes:
> To Mark or anyone who can modify the beadarray package,
>
> I am having further problems with the example data in the beadarray
package.
> Using R2.4.0 or R2.5.0dev on Windows XP.
> > sessionInfo()
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC
_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australi
a.1252
>
> attached base packages:
> [1] "tools" "methods" "stats" "graphics" "grDevices"
"utils"
> "datasets" "base"
>
> other attached packages:
> beadarray affy affyio Biobase limma
> "1.2.1" "1.12.0" "1.2.0" "1.12.2" "2.9.1"
>
> When I do the following:
> =================
> > library(beadarray)
> > targets = readBeadSummaryTargets("targets.txt")
> > targets
> DataFile SampleSheet QCInfo
> 1 raw_data.csv raw_data_sample_sheet.csv raw_data_qcinfo.csv
> >
> > BSData <- readBeadSummaryData(targets)
> Reading file raw_data.csv
> Reading file raw_data.csv
> > QCInfo(BSData)
> <environment: 0x042ad370="">
> =================
> When I load the BSData item I get the following:
> =================
> > library(beadarray)
> > data(BSData)
> > QCInfo(BSData)
> $Signal
> Biotin cy3_high cy3_low cy3_med gene hs house
labeling
> mm pm negative
> 1475542110_F 7551.0 32436.0 816.6 11178.2 205.8 29498.3 7914.2
92.9
> 3584.5 21807.1 94.4
> ...for 18 lines
> $StDev
> Biotin cy3_high cy3_low cy3_med gene hs house
labeling mm
> pm negative
> 1475542110_F 675.2 9453.7 155.3 3303.9 0.5 5463.8 2405.3
7.6 2978.1
> 13118.4 11.8
> ...for 18 lines
> $Detection
> Biotin cy3_high cy3_low cy3_med gene hs house
labeling mm pm
> negative
> 1475542110_F 1 1 1 1 0.6499011 1 1
0.4153883 1 1
> 0.7470226
> ...for 18 lines
> ==================
> So there is something wrong with QCInfo(BSData) in the first
approach.
>
>
> I have investigated this problem and found that if I change line 54
in
> ExpressionSetIlluminaQC.R from:
>
> QC = assayDataNew(Signal = signal, StDev=var,
Detection=detection,
> storageMode="list")
>
> to
>
> QC = as.list(assayDataNew(Signal = signal, StDev=var,
Detection=detection,
> storageMode="list"))
>
> the problem is fixed. If Mark or anyone else could check this fix
and if they
> agree, please submit this it to the current release and devel
versions of the
> beadarray package, I'm sure it would help others trying to get the
example data
> to work as descibed,
>
> thanks
>
> Keith
>
> ========================
> Keith Satterley
> Bioinformatics Division
> The Walter and Eliza Hall Institute of Medical Research
> Parkville, Melbourne,
> Victoria, Australia
>
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--
Martin T. Morgan
Bioconductor / Computational Biology
http://bioconductor.org
