[BioC] limma - read function

[Sylvain FORET]

TEXTORIS Julien wrote:
> Hi,
> 
> Could someone send me an imagene file as an example ?
> I tried to write a read function for my quantifier software (BZSCAN), 
> and i try to follow the read.imagene function as i also have two 
> separate files. But as i don't know the imagene format, i don't 
> understand all the code of the function, and what i have to change.
> 
> Thanks for your help,
> 
> Julien

What you want to use is read.maimage, not read.imagene, unless your 
software's output is exactly similar to that of Imagene.

Let's assume that your software outputs comma separated files with at 
least 4 columns:
the red channel foreground column called "Cy5F"
the red channel background column called "Cy5B"
the green channel foreground column called "Cy3F"
the green channel background column called "Cy3B".

You just have to do something like that:

 >targets <- readTargets('yourTargets')
 >RG <- read.maimages(targets$FileName,
                      columns=list(Rf="Cy5F",
                                   Gf="Cy3F",
                                   Rb="Cy5B",
                                   Gb="Cy3B"),
                      sep=",")

Of course you can have more column in your datafile and read them to use 
them (eg.) for weighting.

Hope it helps,

SF