[BioC] Limma:What's wrong with my Targets file?

[James Wettenhall]

Hi,

On Mon, 14 Jun 2004, xpzhang wrote:
> using limma. After I read the userguide of limma, I made a Targets
> file.It is just like: 
> SlideNumber	FileName	Cy3	Cy5 
> 1	2004-4-2-cy3(450)-0409-Con-only532.gpr	Con	Blank
> 2	2004-4-2-cy3(450)-0410-A24h-only532.gpr	A1h	Blank
...
<snip>

> And the file's name is Targets.

Do you mean "Targets.txt"?  If in doubt about whether limma is 
accessing the correct file, specify the full filename as an 
argument to readTargets, e.g. 
readTargets("MyTargetsFile.txt")

See ?readTargets for more information.

> But I failed in running limma.This is the result:
> > targets <- readTargets()
> Error in file(file, "r") : unable to open connection

It certainly sounds like limma cannot find your file.  Check 
your current working directory in R, using getwd().  Check that 
your targets file is in that directory and that it is called 
"Targets.txt", or whatever you specify for the file argument of 
readTargets.  (See ?readTargets).

If you still have trouble, check that your targets file is 
tab-delimited (not space-delimited) and that there are no extra 
tabs at the end of rows.

You could also try removing the special characters from your gpr 
filenames, e.g. the parentheses: '(' and ')' but this shouldn't 
really be necessary.

Regards,
James