Hi , I am trying to use a applied biosystems dataset using human genome survey microarray version 2 platform. I tried using the ABarray package and it gives me an error while doing the basic analysis on non-normalised data. I have given the script below with the error. Reading data from C:/Users/jay/Desktop/rawdata/_raw_data_modified.txt ...... This may take several minutes.... Finished data reading. The results will be in the folder: Result_Status/ [1] "Creating plot for Signal Hybridization_Control ..." [1] "Creating plot for Signal Negative_Control ..." [1] "Creating plot for Signal IVT_Kit_Control_BIOB ..." [1] "Creating plot for Signal IVT_Kit_Control_BIOC ..." [1] "Creating plot for Signal IVT_Kit_Control_BIOD ..." [1] "Creating plot for Signal RT_Kit_Control_DAP ..." [1] "Creating plot for Signal RT_Kit_Control_LYS ..." [1] "Creating plot for Signal RT_Kit_Control_PHE ..." Perform basic analysis for non-normalized data ... [1] "Creating barplot for probes detectable ... QC_DetectableProbeSN3" Error in is.null(x) || all.equal(x, y, check.attr = FALSE) : invalid 'y' type in 'x || y' I have checked if the sample names in the data file match with the design file and all of them do. I am stuck at this point. It would be great if someone could me solve this issue Thanks Jay Jayakumar Mani PhD Student Department of Biological Sciences University of Essex Colchester CO4 3SQ United Kingdom ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] on behalf of Mark Dunning [mark.dunning@gmail.com] Sent: 01 May 2013 11:47 To: R; bioconductor at r-project.org Subject: Re: [BioC] beadarray package 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 at="" 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 at="" 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 at="" 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 at 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]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi , I am trying to use a applied biosystems dataset using human genome survey microarray version 2 platform. I tried using the ABarray package and it gives me an error while doing the basic analysis on non-normalised data. I have given the script below with the error. Reading data from C:/Users/jay/Desktop/rawdata/_raw_data_modified.txt ...... This may take several minutes.... Finished data reading. The results will be in the folder: Result_Status/ [1] "Creating plot for Signal Hybridization_Control ..." [1] "Creating plot for Signal Negative_Control ..." [1] "Creating plot for Signal IVT_Kit_Control_BIOB ..." [1] "Creating plot for Signal IVT_Kit_Control_BIOC ..." [1] "Creating plot for Signal IVT_Kit_Control_BIOD ..." [1] "Creating plot for Signal RT_Kit_Control_DAP ..." [1] "Creating plot for Signal RT_Kit_Control_LYS ..." [1] "Creating plot for Signal RT_Kit_Control_PHE ..." Perform basic analysis for non-normalized data ... [1] "Creating barplot for probes detectable ... QC_DetectableProbeSN3" Error in is.null(x) || all.equal(x, y, check.attr = FALSE) : invalid 'y' type in 'x || y' I have checked if the sample names in the data file match with the design file and all of them do. I am stuck at this point. It would be great if someone could me solve this issue Thanks Jay Jayakumar Mani PhD Student Department of Biological Sciences University of Essex Colchester CO4 3SQ United Kingdom