Entering edit mode
> 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