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

STKH (Steen Krogsgaard) stkh at novozymes.com
Mon Jun 7 12:14:41 CEST 2004


I have a bunch of Imagene data files that I want to read into limma
using read.imagene. It all works very nicely like this:

RG<-read.imagene(files), where files is a matrix with two columns and
one row for each array. The names of the two dye-files are in the two

I want to wrap this call into another function in order to do some
processing of the quality flags that Imagene uses (I want to change the
flags into weights). The idea is:

read.my.imagene <-function(files, path = NULL, ext = NULL, names = NULL,
columns = NULL, 
    wt.fun = NULL, verbose = TRUE, sep = "      ", quote = "\"",
exclude.flags=c(1,2,3), ...)
	obj=read.imagene(files=files, path=path, ext=ext, names=names,
columns=columns, wt.fun=wt.fun, verbose=verbose, sep=sep, quote=quote,
	// do some more stuff

but when I call read.my.imagene I get an error "Error in scan(file =
file, what = what, sep = sep, quote = quote, dec = dec,  : 
        line 1 did not have 27 elements". I understand that scan is
complaining about the number of columns in the data file, but I'm really
puzzled why it works when I call read.imagene directly but not when I
call read.my.imagene which then in turn calls read.imagene.

I also tried to copy the source code for read.imagene into a new
function (which I called test.read), and this produced the exact same
error. There were no code changes done, just a copy of the source code
into Notepad (yes, I'm on a Windows box) preceeded by "test.read = ".

I use R 1.9.0 and the latest Bioconductor (downloaded last week).

thanks in advance for any suggestions

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