Hi Mark and Matt, I have four samples with three replicates for which Illumina beadarray expression data was collected. The array design corresponds to the HumanHT12 chip with Humanv4 annotation. I started with beadlevel data with .tif files, .locs files and _perBeadFile.txt and was able to use processSwathData() function to obtain 24 _Swath.tif files. My sampleSheet.csv had issues although I prepared it based on the beadlevel example data you provide. So, I didn't provide this file and used readIllumina() to read the 24 _Swath.tif files. It read the files fine but it's not clear how to combine the two files into one intensity file per array/sample? I would like to create an expressionSet and perform differential expression using limma. I would appreciate any help. Thanks, Raj -- output of sessionInfo(): None -- Sent via the guest posting facility at bioconductor.org.

Hi Raj, You should be able to achieve what you want by using the useSampleFac argument to the summarise function summaryData <- summarize(beadLevelData, useSampleFac=T, sampleFac = rep(LETTERS[1:12], each=2) The resulting summary object should now have 12 arrays rather than 24 Hope this helps, Mark On Fri, Apr 26, 2013 at 3:45 AM, RS [guest] <guest@bioconductor.org> wrote: > > Hi Mark and Matt, > > I have four samples with three replicates for which Illumina beadarray > expression data was collected. The array design corresponds to the > HumanHT12 chip with Humanv4 annotation. > > I started with beadlevel data with .tif files, .locs files and > _perBeadFile.txt and was able to use processSwathData() function to obtain > 24 _Swath.tif files. My sampleSheet.csv had issues although I prepared it > based on the beadlevel example data you provide. So, I didn't provide this > file and used readIllumina() to read the 24 _Swath.tif files. It read the > files fine but it's not clear how to combine the two files into one > intensity file per array/sample? I would like to create an expressionSet > and perform differential expression using limma. > > I would appreciate any help. > > Thanks, > Raj > > > -- output of sessionInfo(): > > None > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]