[BioC] Gene filtering for differential expression (limma)

[Špela Baebler]

Nice to get a reply:-) 
We now have a problem which is more statistics than R. We have a problem with creating a design and contrast matrix. 

If we just want to compare vithin one variety, it is easy
design <- c(1,-1,1,-1,1)
where we just take into the account the dye swaps. 

We couldn't find any example that would fit our experimental design in Limma users Guide, since we don't have a common reference for all arrays.
So do you have a suggestion for contrast matrix if we want to compare the 4 varieties?

Waiting for answers...

Spela

P.S:: Is there someone using TIGR potato microarrays out there?

-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sent: Thursday, July 21, 2005 12:58 AM
To: Špela Baebler
Cc: bioconductor at stat.math.ethz.ch
Subject: [BioC] Gene filtering for differential expression (limma)

> Date: Tue, 19 Jul 2005 10:53:37 +0200
> From: ?pela Baebler <Spela.Baebler at nib.si>
> Subject: [BioC] Gene filtering for differential expression (limma)
> To: <bioconductor at stat.math.ethz.ch>
>
> Hello everyone!
>
> We are struggling to implement R for the analysis of two color cDNA microarrays.
>
> Each microarray is hybridised with treated control plant RNA. There are 5 biological repetitions,
> they also include dye swaps. We would like to compare 4 groups of plants (cultivars) having the
> same treatment, meaning altogether the experiment has 20 microarrays.  Initial quality control and
> spot filtering are performed in image analysis program.
>
> We are trying to do further analysis with limma package, although we are not experienced R users.
>
> We are wondering is limma the appropriate package for such an experimental outline, or we should
> try any other packages? Which ones would you recommend?

limma is certainly intended to address this sort of experiment.  Have you run into problems or are
you just trying to get an idea of the alternatives?

Gordon

> Thanks for any answers/comments,
>
> Spela Baebler
>
> National Institute of Biology
> Dept. of Plant Physiology and Biotechnology
> Ljubljana
> SLOVENIA