Question: agi4x44preprocess
0
gravatar for Neel Aluru
10.0 years ago by
Neel Aluru450
United States
Neel Aluru450 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
agi4x44preprocess • 602 views
ADD COMMENTlink modified 10.0 years ago by Tobias Straub410 • written 10.0 years ago by Neel Aluru450
Answer: agi4x44preprocess
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gravatar for Tobias Straub
10.0 years ago by
Tobias Straub410
Tobias Straub410 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
ADD COMMENTlink written 10.0 years ago by Tobias Straub410
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
ADD REPLYlink written 10.0 years ago by Neel Aluru450
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
ADD REPLYlink written 10.0 years ago by Michael Dondrup140
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