[BioC] beadarray and BeadStudio v.2.3.41

[Mark Dunning]

Hi Asta,

Thanks for the information about the new version arrays and for the  
data you sent me off the list.

I think the problem with reading bead level data might arise because  
we assumed that the number of beads in the txt files would be the  
same for every array. This was true for example files that Illumina  
gave us a year ago, but the files that are produced by the scanner  
are different.

We are currently working on a new class for bead level data which  
stores everything in an environment where each array is allowed to  
have a different number of beads. The new class will be added to the  
package repository as soon as possible.

Similarly I'm looking into the new bead summary data format and how  
it can be read into beadarray. The quality control file is quite  
problematic because it does not seem to have a fixed format at all!

Regards,

Mark

On 2 Feb 2007, at 12:35, Asta Laiho wrote:

> 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"
>>
>
> #----------------------------------------------------
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/ 
> gmane.science.biology.informatics.conductor