[BioC] beadarray example data problem 2

[Keith Satterley]

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_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