The best resource that we have is the vignette for the BeadArrayUseCases pacakge. It accompanies our paper that came out in PLoS one 'BeadArray Expression Analysis Using Bioconductor' Regards, Mark On Tue, Apr 30, 2013 at 9:12 PM, R <rs2206@gmail.com> wrote: > Hi Mark, > > Thank you, it worked! > > It would be great if you could point me to tutorials that you have > developed for analyzing Illumina beadarrays going from raw tif files > to qc to differential expression. The vignettes are helpful but > sometimes it's not clear how exactly to go about. > > best, > Raj > > > On Tue, Apr 30, 2013 at 1:48 PM, Mark Dunning <mark.dunning@gmail.com> > wrote: > > 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]]