hi, there: > targets = read.targets("1.txt") > data(targets) > targets FileName Treatment GErep Subject Array Ast Ast.txt st 1 A 1 Bst Bst.txt st 1 B 1 Aunst Aunst.txt unst 2 A 1 Bunst Bunst.txt unst 2 B 1 THEN, when I use this function: > dd=read.AgilentFE(targets,makePLOT=TRUE) ERROR MESSAGE is : Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : cannot open file 'Ast.txt': No such file or directory is there anybody know what's wrong with my work? Thanks in advance, Xiang

Hi Xiang, Try with > dd=read.AgilentFE(targets$FileName,makePLOT=TRUE) If that does not work , try with "path" attribute. Then the above command becomes, > dd <- read.AgilentFE(targets$FileName,makePLOT=TRUE, path="path to the FE files") I hope you are familiar with path naming in different OS. Regards, Prashantha --- On Tue, 6/23/09, xiangxue Guo <xiangxue_guo@yahoo.com> wrote: From: xiangxue Guo <xiangxue_guo@yahoo.com> Subject: [BioC] Error message of read.AgilentFE() using package Agi4x44PreProcess To: bioconductor@stat.math.ethz.ch Date: Tuesday, June 23, 2009, 3:02 AM hi, there: > targets = read.targets("1.txt") > data(targets) > targets        FileName Treatment GErep Subject Array Ast     Ast.txt        st     1       A     1 Bst     Bst.txt        st     1       B     1 Aunst Aunst.txt      unst     2       A     1 Bunst Bunst.txt      unst     2       B     1 THEN, when I use this function: > dd=read.AgilentFE(targets,makePLOT=TRUE) ERROR MESSAGE is : Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : cannot open file 'Ast.txt': No such file or directory is there anybody know what's wrong with my work? Thanks in advance, Xiang _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Hi, As I understand, you want to read the files that you have in your target file, '1.txt'. Apparently, when you use 'data(targets)' the target file that is included in the package as an example is loaded and substitute your targets variable, then the read.AgilentFE() function attempts to read the files Ast.txt , etc ..., that you obviously don't have. Don't use data(targets), or use another name for your targets varialble, my.targets = read.targets("1.txt") if you type my.targets, you will have to see what is in your target file, and not something else my.dd=read.AgilentFE(my.targets,makePLOT=TRUE) p.- On Mon, Jun 22, 2009 at 11:02 PM, xiangxue Guo <xiangxue_guo@yahoo.com>wrote: > > hi, there: > > > targets = read.targets("1.txt") > > data(targets) > > targets > FileName Treatment GErep Subject Array > Ast Ast.txt st 1 A 1 > Bst Bst.txt st 1 B 1 > Aunst Aunst.txt unst 2 A 1 > Bunst Bunst.txt unst 2 B 1 > > THEN, when I use this function: > > > dd=read.AgilentFE(targets,makePLOT=TRUE) > > ERROR MESSAGE is : > > Error in file(file, "r") : cannot open the connection > In addition: Warning message: > In file(file, "r") : cannot open file 'Ast.txt': No such file or directory > > is there anybody know what's wrong with my work? > > Thanks in advance, > > Xiang > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]