[BioC] PreFiltering probe in microarray analysis
stephanie.pierson at etumel.univmed.fr
Wed Jun 1 14:58:47 CEST 2011
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 ?
Universite de la Mediterranee (Aix-Marseille II)
Master 2 Pro Bioinformatique et Génomique
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