[BioC] Gene filtering for differential expression (limma)

[Špela Baebler]

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?


Thanks for any answers/comments,


Spela Baebler

National Institute of Biology
Dept. of Plant Physiology and Biotechnology
Ljubljana
SLOVENIA
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