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" > #----------------------------------------------------

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