[BioC] Newbie!

Jean Yee Hwa Yang jean at biostat.ucsf.edu
Fri Aug 15 00:52:28 MEST 2003

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

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.



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
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