[BioC] Reading Imagene files with read.imagene in limma

[James Wettenhall]

Steen,

On Mon, 7 Jun 2004, STKH (Steen Krogsgaard) wrote:
>     wt.fun = NULL, verbose = TRUE, sep = "      ", quote = "\"",
> exclude.flags=c(1,2,3), ...)

Perhaps you took code from read.imagene using an unreliable 
method like typing "read.imagene" at the R prompt and pressing 
enter or by typing "edit(read.imagene)" and seeing the code in 
a text editor like Notepad.  One reason why both of these 
methods are unreliable is that (at least on Windows), they will 
try to convert the special tab character "\t" in sep="\t" to 
an actual tab:
"	"

A more reliable way is to download the source of limma (the 
.tar.gz file) and find the read.imagene function in R/read.R 
using a reliable text editor.

So, try changing   sep="	" to sep="\t".

Could this be the problem?

Regards,
James