Question: limma - read function
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gravatar for TEXTORIS Julien
14.0 years ago by
TEXTORIS Julien160 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
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ADD COMMENTlink modified 14.0 years ago by Sylvain FORET10 • written 14.0 years ago by TEXTORIS Julien160
Answer: limma - read function
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gravatar for Sylvain FORET
14.0 years ago by
Sylvain FORET10 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$FileName, columns=list(Rf="Cy5F", Gf="Cy3F", Rb="Cy5B", Gb="Cy3B"), sep=",") Of course you can have more column in your datafile and read them to use them (eg.) for weighting. Hope it helps, SF
ADD COMMENTlink written 14.0 years ago by Sylvain FORET10
Sylvain FORET wrote: > TEXTORIS Julien wrote: > >> Hi, >> >> Could someone send me an imagene file as an example ? >> I tried to write a read function for my quantifier software (BZSCAN), >> and i try to follow the read.imagene function as i also have two >> separate files. But as i don't know the imagene format, i don't >> understand all the code of the function, and what i have to change. >> >> Thanks for your help, >> >> Julien > > > What you want to use is read.maimage, not read.imagene, unless your > software's output is exactly similar to that of Imagene. > > Let's assume that your software outputs comma separated files with at > least 4 columns: > the red channel foreground column called "Cy5F" > the red channel background column called "Cy5B" > the green channel foreground column called "Cy3F" > the green channel background column called "Cy3B". > > You just have to do something like that: > > >targets <- readTargets('yourTargets') > >RG <- read.maimages(targets$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 ? Julien
ADD REPLYlink written 14.0 years ago by TEXTORIS Julien160
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