Question: Is a set of four arrays suitable for RMA analysis?
16.5 years ago by
Wei, Wenbin • 50
Wei, Wenbin • 50 wrote:
Hello, I have a set of four Affymetrix HG-Focus arrays (including two controls and two treatments) to be analyzed. I would like to know whether a set of four arrays is suitable for RMA analysis. In Irizarry et al. (http://www.biostat.jhsph.edu/~ririzarr/papers/affy1.pdf <http: www.biostat.jhsph.edu="" ~ririzarr="" papers="" affy1.pdf=""> ), the minimum number of arrays in a set subjected to RMA analysis was five. In dChip manual, it is mentioned that "For better model fitting and outlier detection, the number of arrays in a dChip group is desired to be more than 5. " (http://biosun1.harvard.edu/complab/dchip/prepare%20data.htm <http: biosun1.harvard.edu="" complab="" dchip="" prepare%20data.htm=""> ). Has anybody compared various methods available in the Affy package for the analysis of a set of four arrays? Which is the best? Wenbin Wei Division of Cancer Studies Birmingham University Birmingham, B15 2TT UK [[alternate HTML version deleted]]
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