[BioC] limma - read function

TEXTORIS Julien julien.textoris at gmail.com
Wed Sep 14 06:11:30 CEST 2005

Sylvain FORET wrote:

> 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
Thanks, Sylvain,

i knew that option, but my data are in two separate files, for complex 
hybridation(sample), whih i call R, and vector hybridation, chich i call 
G. In fact i could write a script to first parse the two files and 
create a temporary file that i would read like that. But i think it 
would be easier just to type :

read.maimage(files, source="bzscan"). And for that, i simply have to 
rewrite the read.imagene function into read.bzscan. Don't you agree ?


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