Dear David,

Thank you for your help. Can you please tell me how do you exactly edit the
source code of a package and the use this 'modified package'?

For example, I was wondering if it is possible to add some 'filter by
flags' option in limma so that I can filter out probes that do not meet the
specified flag criteria from my Agilent single color microarray data set (
I am not sure if limma already has this function). Is this possible in
limma?

Thanks,

Karthik

On Sat, Jun 16, 2012 at 4:06 PM, David Westergaard <david@harsk.dk> wrote:

> Dear Karthik,
>
> If you go to the Bioconductor website (www.bioconductor.org), and
> search for a package, (e.g. limma:
> http://www.bioconductor.org/packages/release/bioc/html/limma.html), at
> the very bottom you have to option to download the source. If you are
> just curious as to how the code looks, you can also view the source by
> calling the function without any parameters. For instance, just
> running 'lmFit' would return the functions source code.
>
> Yes, it is also possible to edit the source code.
>
> Best,
> David
>
> 2012/6/16 Karthik K N <karthikuttan@gmail.com>:
> > Hello members,
> >
> > I am using AgiMicroRna and Limma packges for analyzing Agilent microarray
> > data. I would like to know if it is possible to have access to the source
> > codes of these packages so that I can better understand what is goind on
> in
> > the background when we call each functions.
> >
> > Also, is it possible to edit the source code and run the package?
> >
> > Thanks a lot in advance,
> >
> > Regards,
> >
> > --
> > Karthik
> >
> >        [[alternative HTML version deleted]]
> >
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