[BioC] beadarray and BeadStudio v.2.3.41

[Asta Laiho]

I have just received data from Illumina HumanRef-8_V2 Expression BeadChips. The scanner data was processed with the new BeadStudio v.2.3.41. 

First I tested analyzing the bead level data with beadarray. Reading only one .tif and .txt  file at a time worked fine, but when there were more files, the function failed.

There was also a problem in reading the bead summary data output from the updated BeadStudio. The main problem is that the new BeadStudio does not produce QCInfo file in the same format anymore. When I used old format qcinfo file, I found out that there was a problem also in the format of the raw data file. The error messages and session info are shown below.

- Asta Laiho

#------------------------------------------------------------------------------------------------
Reading bead level data:
#------------------------------------------------------------------------------------------------
> library(beadarray)
>
> targets <- readBeadTargets("beadTargets.txt")
> targets
                Image1           xyInfo SAMPLE
1 1234567899_A_Grn.tif 1234567899_A.txt      A
2 1234567899_B_Grn.tif 1234567899_B.txt      B

> BLData <- readBeadLevelData(targets)
Reading pixels of 1234567899_A_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Error in BLData at ProbeID[, i] <- dat1$ProbeID[ord] 
        number of items to replace is not a multiple of replacement length
>     

#-------------------------------------------------------------------
Reading bead summary data:
#-------------------------------------------------------------------

targets<-readBeadSummaryTargets("targets.txt")
> targets
                DataFile                 SampleSheet
1 Experiment RawData.csv Experiment Sample Sheet.csv
                                QCInfo
1 Experiment BeadStudio 1.5_qcinfo.csv
> BSData<-readBeadSummaryData(targets)
Reading file  Experiment RawData.csv
Error in readBeadSummaryData(targets) : Could not find any columns called TargetID
In addition: Warning message:
number of items read is not a multiple of the number of columns


#-------------------------------------------------------------------
Session info:
#-------------------------------------------------------------------
> sessionInfo()
R version 2.4.0 (2006-10-03)
x86_64-redhat-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=en_US.UTF-8;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"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
beadarray      affy    affyio   Biobase     limma
  "1.2.2"  "1.12.0"   "1.0.0"  "1.12.0"   "2.9.1"
>   

#----------------------------------------------------