Thank you Matt!! That helps! Hajar On Oct 4, 2010, at 1:29 AM, Matthew Ritchie wrote: > Dear Hajar, > > If this is the same data you mailed the list about the other day, make > sure the 'arrayNames' you are specifying are the full names (probably > something like '5513091009_A_1_perBeadFile.txt', > '5513091009_A_2_perBeadFile.txt' for your first sample if you have WG-6 > BeadChips, etc.) > > Also make sure that all of these files are available in the current > working directory - you can check this with > > dir(pattern="*perBeadFile.txt") > > If they aren't, change the working directory using the setwd() function. > > Best wishes, > > Matt > >> Hi everyone, >> >> I practiced using "Analysing Illumina bead-based data using beadarray by >> Richie & Dunning with the SAMExample dataset. However, when exploring my >> own beadarraydata I found that my raw data files are txt files and not csv >> (as they were in the practical). >> I was able to read the metrics.txt file (this file gives me the date of >> analysis, beadchip, section...etc), but when I try to use: >> >> BLData = readIllumina(arrayNames = metrics$arrayID, textType = ".txt", >> metrics = metrics, backgroundMethod = "none") >> >> I get this response: >> Found 0 arrays >> Error in seq.default(1, length(tmp), by = 3) : wrong sign in 'by' argument >> >> I've tried replacing arrayID with Beadchip, since it is used in the >> metrics file, and still it gives me the same message. There should be 24 >> arrays. Is there another function to read the arrays in R? >> >> Thank you in advance, >> >> Hajar >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:6}}