[BioC] PreFiltering probe in microarray analysis

Stephanie PIERSON stephanie.pierson at etumel.univmed.fr
Wed Jun 1 14:58:47 CEST 2011

Hello everybody,

I am a french student in bioinformatic. I have to analyze microarray  
data and I have some questions about prefiltering genes.
The dataset that I have to analyze consist in 8 microarray, i have 4  
times points and 2 replicats for each time point. Agilent's two color  
microarray  (Whole Mouse Genome (4x44K) Oligo Microarrays) were used  
for the analysis. We are searching for genes that are differentially  
expressed between two conditions (for example C1 and C2) at the  
different time points and genes that are differentially expressed in  
one condition (C1 or C2) over time .
I have chosen LIMMA to perform the statistical analysis because I read  
in papers (Jeanmougin et al. PLoS ONE, Jefferey and al. BMC  
bioinformatic 2006,7/359  ) that it work better in experiment with few  
replicate per conditions.
I perfom the statistical analysis on the whole data set ( more than 37  
000 genes ), but I have high corrected p value after multiple testing  
correction (benjamini hochberg ). I would like to prefilter genes  
before statistical analysis, but I don't know how to do this. I read  
in Bourgon's paper that we can filter on the overall variance or on  
the overall mean, but in my case, with few replicates, how can I do ?  
In more, in this paper, it is not recommended to combine limma with a  
filtering procedure ...
Someone can help me please ?

Thank you,
Best wishes

Stéphanie PIERSON
Universite de la Mediterranee (Aix-Marseille II)
Master 2 Pro Bioinformatique et Génomique

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