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]]

i use RMA if i have 2 or more arrays. the roc curves in this paper http://nar.oupjournals.org/cgi/content/full/31/4/e15?ijkey=EAz2cYYbEWQ rE&keytype=ref&siteid=nar are based on 2 array comparisons. On Tue, 17 Jun 2003, Wei, Wenbin 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >