[BioC] Using limma with Agilent array data

[Sean Davis]

On Mon, Jun 2, 2008 at 6:26 PM, Anh Tran <popophobia at gmail.com> wrote:
> Hi all,
> We've been using Agilent Scanner and Feature Extraction from Agilent.
>
> I'm wondering if there's a way to import these data into limma. Out of the
> three required input files (GAL file, Targets file, Spot-type file), we only
> have GAL file. FE gives us SHP file and a txt file witn compiled list of
> probes and its reading. We are doing 2 color microarray btw.
>
> If you know any detail, please help us.
>
> Also, is it possible to group a certain probes together as one entity (they
> are expected to have the same result)? And is it possible to give a set of
> probes as normalizing set for limma (set ratio to 1-1)?

Limma offers many options for normalization and choosing probes for
normalization.  I would definitely put some thought into the rationale
for using a subset of the probes, though.

> I've been looking through the manual but could not find any reference about
> Agilent output file.

You'll need to look at the help, also.  Look at the help for
read.maimages().  Let us know if that doesn't work by posting the code
you tried, any errors, and of course the output of sessionInfo().

Sean