Hi, looks like you just got a '.' too much in the header line in your targets file: 'File.Name' vs 'FileName'. Best Am 28.10.2009 um 20:17 schrieb Neel Aluru: > Hi Tobias, > > Thanks for your help. I tried your suggestion and it keeps giving me > a new error message. Here are the details of my trials. > > > library("Agi4x44PreProcess") > Loading required package: Biobase > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > Loading required package: limma > Loading required package: annotate > Loading required package: AnnotationDbi > Loading required package: genefilter > > > getwd() > [1] "/Users/Neel/agilent" > > targets=read.targets(infile="infile.txt") > > Target File > X File.Name Treatment GErep > 1 cont1 conta.txt control 1 > 2 cont2 contb.txt control 2 > 3 cont3 contc.txt control 3 > 4 cont4 contd.txt control 4 > 5 pcb1 pcba.txt pcb 1 > 6 pcb2 pcbb.txt pcb 2 > 7 pcb3 pcbc.txt pcb 3 > 8 pcb4 pcbd.txt pcb 4 > > > read.AgilentFE(targets, makePLOT) > Error in read.maimages(files = targets$FileName, source = "agilent", > other.columns = list(IsFound = "gIsFound", : > Must specify input files > > It is able to recognize the infile which has all the details of the > files. Also, all the files are in the same directory. Cannot > understand why it cannot recognize the files. > > Any help will be greatly appreciated. > > Sincerely, Neel > > On Oct 27, 2009, at 11:59 AM, Tobias Straub wrote: > >> what about >> >targets = read.targets(infile="infile.txt") >> >read.AgilentFE(targets, makePLOT) >> >> best >> T. >> >> On Oct 27, 2009, at 4:43 PM, Neel Aluru wrote: >> >>> Hello, >>> >>> I am just beginning to work with Bioconductor and started having >>> issues, which I think are minor but cannot figure out myself. I >>> started using Agi4x44preprocess and the first step went fine. That >>> is >>> >>> >targets = read.targets(infile="infile.txt") >>> This loads my list of files and treatments as a data.frame. >>> My problem is with the next step. >>> >read.AgilentFE(infile, makePLOT) >>> >>> I get an error message, "Error in is(targets, "data.frame") : >>> object 'infile' not found". I have the infile and all the >>> agilentFE text files in my working directory. Not sure where I am >>> doing it wrong. >>> >>> Any help is appreciated. >>> >>> Sincerely, Neel >>> >>> Neel Aluru >>> Postdoctoral Scholar >>> Biology Department >>> Woods Hole Oceanographic Institution >>> Woods Hole, MA 02543 >>> USA >>> >>> _______________________________________________ >>> 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 >> >> ---------------------------------------------------------------------- >> Dr. Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, >> M?nchen D >> >> >> >> >> >> > > Neel Aluru > Postdoctoral Scholar > Biology Department > Woods Hole Oceanographic Institution > Woods Hole, MA 02543 > USA > 508-289-3607 > > _______________________________________________ > 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 Michael Dondrup, Ph.D. Bergen Center for Computational Science Computational Biology Unit Unifob AS - Thorm?hlensgate 55, N-5008 Bergen, Norway Phone: +47 55584029 Fax: +47 55584295