Hello, I am trying to work out how to use the Beadarray package and am following the 'Expression analysis' exercise in the manual. When I followed the instructions and typed the command > BLData = readIllumina(arrayNames = targets$arrayID, textType = ".csv", + targets = targets, backgroundMethod = "none") I got the error message Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'NA/NA': No such file or directory A Google search suggested that the problem was to do with the recent beadarray upgrade and that I needed to specify the files I wanted to read in by using the sectionNames argument. So I tried this: > BLData = readIllumina(arrayNames = targets$arrayID, sectionNames = c("1318740_R007_C007", "1318740_R008_C006", "1318758_R002_C002", "1318758_R007_C004", "1318782_R004_C012", "1318791_R001_C007", "1318791_R002_C006", "1318803_R008_C010", "1328198_R002_C002", "1328227_R002_C002", "1328227_R007_C004"), textType = ".csv", targets = targets, backgroundMethod = "none") and I got the error message Error in data.frame(directory = dir, sectionName = sectionNames[validNames], : arguments imply differing number of rows: 1, 0 Can anyone advise as to what the problem is? I'm sorry if this is a stupid question, in all honesty I don't really understand what the readIllumina command does and I can't seem to find a clear answer anywhere. Thanks very much in advance, Sarah [[alternative HTML version deleted]]

Hi Sarah, Assuming you're using the latest version of beadarray (version >= 2.0.0), I'm afraid the information in the SAM Example work flow is rather outdated. Many of the arguments to functions have changed and a better starting point for getting to grips with beadarray is to take a look at the vignette, which you can either download from here: http://bioconductor.org/help/bioc-views/2.7/bioc/html/beadarray.html or access via the command vignette("beadlevel"). The data itself is also quite outdated. We haven't seen Illumina data with a .csv extension for a number of years, so beadarray by default looks for .txt files, which is something we may need to make more flexible. You can download some more recent examples of data from here: http://www.compbio.group.cam.ac.uk/Resources/baloc/, although you'll need to BeadDataPackR package to extract the data. I'll update our webpage to reflect the fact that the scripts are out of date, sorry that we haven't done that already. I hope that's of some help, On Mon, Feb 7, 2011 at 4:57 PM, Sarah Allen <sa413@cam.ac.uk> wrote: > Hello, > > I am trying to work out how to use the Beadarray package and am > following the 'Expression analysis' exercise in the manual. > > When I followed the instructions and typed the command > > > BLData = readIllumina(arrayNames = targets$arrayID, textType = > ".csv", > + targets = targets, backgroundMethod = "none") > > I got the error message > > Error in file(file, "rt") : cannot open the connection > In addition: Warning message: > In file(file, "rt") : cannot open file 'NA/NA': No such file or > directory > > A Google search suggested that the problem was to do with the recent > beadarray upgrade and that I needed to specify the files I wanted to > read in by using the sectionNames argument. > > So I tried this: > > > BLData = readIllumina(arrayNames = targets$arrayID, sectionNames = > c("1318740_R007_C007", "1318740_R008_C006", "1318758_R002_C002", > "1318758_R007_C004", "1318782_R004_C012", "1318791_R001_C007", > "1318791_R002_C006", "1318803_R008_C010", "1328198_R002_C002", > "1328227_R002_C002", "1328227_R007_C004"), textType = ".csv", targets > = targets, backgroundMethod = "none") > > and I got the error message > > Error in data.frame(directory = dir, sectionName = > sectionNames[validNames], : > arguments imply differing number of rows: 1, 0 > > Can anyone advise as to what the problem is? I'm sorry if this is a > stupid question, in all honesty I don't really understand what the > readIllumina command does and I can't seem to find a clear answer > anywhere. > > Thanks very much in advance, Sarah > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- Mike Smith PhD Student Computational Biology Group Cambridge University [[alternative HTML version deleted]]

Mike Smith <grimbough at="" ...=""> writes: > > Hi Sarah, > > Assuming you're using the latest version of beadarray (version >= 2.0.0), > I'm afraid the information in the SAM Example work flow is rather outdated. > Many of the arguments to functions have changed and a better starting point > for getting to grips with beadarray is to take a look at the vignette, which > you can either download from here: > http://bioconductor.org/help/bioc-views/2.7/bioc/html/beadarray.html or > access via the command vignette("beadlevel"). > > The data itself is also quite outdated. We haven't seen Illumina data with > a .csv extension for a number of years, so beadarray by default looks for > .txt files, which is something we may need to make more flexible. You can > download some more recent examples of data from here: > http://www.compbio.group.cam.ac.uk/Resources/baloc/, although you'll need to > BeadDataPackR package to extract the data. > > I'll update our webpage to reflect the fact that the scripts are out of > date, sorry that we haven't done that already. > > I hope that's of some help, > > Thanks very much for the advice. I had an inkling the manual was outdated wrt the current version but I couldn't find anything more up-to-date on the bioconductor site so I thought I'd try starting with that/it was as good a place as any (I have no experience of either R or array analysis so I'm learning from scratch!). Thanks again, Sarah