Hi, there appears to be a bug in the arrayQuality package, specifically the agQuality function which traces back to the function read.Agilent in the marray package. If I specify a path for the location of Agilent microarray files to process which is not the current working directory (path=".", and without specifying 'gnames' information) then I get the following error; >agQuality(fnames=targets$Filename, path=dataDir, resdir = diagPlotDir) [1] "Starting agQuality..." Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : cannot open file '[FILE.txt]': No such file or directory > traceback() 4: file(con, "r") 3: readLines(fullnames[1], n = 100) 2: read.Agilent(fnames = fnames[1], path = path, DEBUG = DEBUG) 1: agQuality(fnames = targets$Filename, path = dataDir, resdir = diagPlotDir) > find("read.Agilent") [1] "package:marray" In 'read.Agilent', the 'fullnames' vector defined on line 15 does not contain fullpath information ('fullfnames') so the readLines function on line 24 fails. If 'gnames' was specified it would probably work. A hack to get it going was to make a symbolic link for the first file to read in the description information from the first file. ln -s /full/path/to/first/file file This temporary workaround works without modifying any R code. If I try putting the full path name 'fnames' in read.Agilent with 'path=NULL' as suggested in help(read.Agilent); > agQuality(fnames=file.path(dataDir, targets$Filename), path=NULL, resdir = diagPlotDir) [1] "Starting agQuality..." Reading ... .//[PATH TO FILE] Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : cannot open file './/[PATH TO FILE]': No such file or directory > > traceback() 6: file(file, "r") 5: read.table(f, skip = skip2, header = TRUE, sep = sep, quote = quote, check.names = FALSE, as.is = TRUE, comment.char = "", nrows = nspots, ...) 4: read.marrayRaw(fnames = "/[PATH TO FILE]", path = ".", name.Gf = "gMedianSignal", name.Gb = "gBGMedianSignal", name.Rf = "rMedianSignal", name.Rb = "rBGMedianSignal", layout = <s4 object="" of="" class="" "marraylayout"="">, gnames = <s4 object="" of="" class="" "marrayinfo"="">, notes = "Agilent Data", skip = 9, sep = "\t", quote = "\"", DEBUG = FALSE) 3: do.call("read.marrayRaw", maRaw.args) 2: read.Agilent(fnames = fnames[1], path = path, DEBUG = DEBUG) 1: agQuality(fnames = file.path(dataDir, targets$Filename), path = NULL, resdir = diagPlotDir) Marcus > sessionInfo() R version 2.7.0 (2008-04-22) powerpc-apple-darwin8.10.1 locale: C attached base packages: [1] grid tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] arrayQuality_1.19.0 RColorBrewer_1.0-2 gridBase_0.4-3 [4] hexbin_1.14.0 lattice_0.17-6 convert_1.16.0 [7] Biobase_2.0.1 marray_1.19.0 limma_2.14.1 > The contents of this e-mail are privileged and/or confid...{{dropped:5}}