Dear Members, I imported the CEL files with the ReadAffy() command. Using head() I got following error term: In x[seq_len(n)] : The use of abatch[i,] and abatch[i] is deprecated. Please use abatch[,i] instead. Using the command : mm(celfiles,'10700055')[1:3,] gives the NA in Mismatch data. ControlW_D3.CEL ED_01_Kd5_09_10_28.CEL ED_02_Kd14_02_03_04.CEL 107000551 NA NA NA 107000552 NA NA NA 107000553 NA NA NA Is there any coincidence between these two commands. How can I convert the abatch[i] format into the abatch[,i] format. Thanks for your attention Mrs: Kammermeier [[alternative HTML version deleted]]

Hi Mrs. Kammermeier, On 3/7/2013 4:29 AM, Antje Kammermeier wrote: > Dear Members, > > I imported the CEL files with the ReadAffy() command. Using head() I got > following error term: This statement is completely vague. What type of celfiles? Using head() on what? When asking questions you need to be much more descriptive. So if I put on my Carnack the Magnificent hat, I can divine several things. First, you used head() on the AffyBatch object you got from running ReadAffy() on your celfiles. In addition, you wanted to see the 'head' of the values that were read in. As you have found, you can't do this. If you just want to see numbers, you can use head(exprs(celfiles)) if you want PM values head(pm(celfiles)) > > In x[seq_len(n)] : > The use of abatch[i,] and abatch[i] is deprecated. Please use abatch[,i] > instead. > > Using the command : mm(celfiles,'10700055')[1:3,] > gives the NA in Mismatch data. > > ControlW_D3.CEL ED_01_Kd5_09_10_28.CEL ED_02_Kd14_02_03_04.CEL > 107000551 NA NA NA > 107000552 NA NA NA > 107000553 NA NA NA > > Is there any coincidence between these two commands. How can I convert the > abatch[i] format into the abatch[,i] format. I can further divine that you are using a random-primer based array (as compared to the 3'-biased arrays). In which case you should note that none of the random-primer based arrays have MM probes. If you had done pm(celfiles,'10700055')[1:3,] you would see some data. Best, Jim > > > Thanks for your attention > > Mrs: Kammermeier > > [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099