[BioC] how to use limma on this format

[Weiwei Shi]

Thanks.

That should solve my problem. Sorry I did not read carefully before I posted.

On 7/17/07, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> Weiwei Shi wrote:
> > Hi there
> >
> > thanks Saroj for the reply.
> >
> > But I think I did not clearify my question: I knew it needs a
> > source=?, while in my case, it seems the format does not match any of
> > the available. So I am asking if I need to create by myself the output
> > from this read.maimages, i.e. RGList or if there is another way. I
> > don't know what format this data belongs to.
>
> Hi, Weiwei.  You will probably benefit from a quick read of the
> read.maimages help.
>
> <quote>
>  columns: list with fields 'R', 'G', 'Rb' and 'Gb' giving the column
>           names to be used for red and green foreground and background
>           or, in the case of Imagene data, a list with fields 'f' and
>           'b'.  This argument is optional if 'source' is specified,
>           otherwise it is required.
>
> other.columns: character vector of names of other columns to be read
>           containing spot-specific information
>
> annotation: character vector of names of columns containing annotation
>           information about the probes
> </quote>
>
> So, you can specify any columns you like.  Also, if there is a header to
> the file as in most Agilent files, you will want to pass skip=9 to
> read.maimages which, according to the help for read.maimages, will be
> passed along to read.table.
>
> I hope that clarifies things a bit.
>
> Sean
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III