[BioC] beadarray example data problem 2

[Mark Dunning]

Hi Keith and Martin,

Thanks for pointing out the problem with the package. I will make the change
from storageMode to storage.mode asap. Obviously I had been using the
correct name at some point but changed when I re-wrote the functions. I'm
surprised it didn't throw any warning message about not recognising a
parameter called storageMode though?

Mark

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Martin
Morgan
Sent: 30 October 2006 05:36
To: keith at wehi.edu.au
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] beadarray example data problem 2


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_MONETAR
Y=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.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

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