[BioC] how to use limma on this format

[Sean Davis]

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