When I'm trying to read in the data from a gpr- file, I use the command widget.marrayRaw("the_name_of_the_file") and I get the widget window. I fill in the column names for the different catagories (F532, B532, F635, B635) and I try to build, but I get the error message "Error in readLines(con, n, ok) : `con' is not a connection" Is there anything fundamental that I'm missing? Do I have to make a Layout first? If I try to read the data with read.GenePix("name_of_file") -> objectname, I don't get an errormessage but when I look at the information about the data it doesn't contain number of spots or any rows and columns. Do I have to import the Layout at first or ...? /Desperate and newbie! /Marcus

Hi Marcus, If you have gpr files, the easiest way to get started is to use the function gpTools. I will also infer the layout information from your gpr or gal file. Try placing all your gpr files in one directory, start R and run library(marrayTools) data <- gpTools() data will be a marrayNorm object If you like to get the unnormalized data (marrayRaw object) use data <- gpTools(raw=TRUE) see help(gpTools) for more information. Cheers Jean On Thu, 14 Aug 2003, Marcus wrote: > When I'm trying to read in the data from a gpr- file, I use the command > widget.marrayRaw("the_name_of_the_file") and I get the widget window. I > fill in the column names for the different catagories (F532, B532, F635, > B635) and I try to build, but I get the error message "Error in > readLines(con, n, ok) : `con' is not a connection" > > Is there anything fundamental that I'm missing? Do I have to make a Layout > first? > > If I try to read the data with read.GenePix("name_of_file") -> objectname, > I don't get an errormessage but when I look at the information about the > data it doesn't contain number of spots or any rows and columns. Do I have > to import the Layout at first or ...? > > /Desperate and newbie! > > /Marcus > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >