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I think you are asking whether limma should be used to select differentially expressed genes before attempting a multivariate method such as factor analysis. Factor analysis will be limited by the problem of having fewer samples than genes. Hence, preselecting a smaller set of genes is definitely helpful. --Naomi At 07:52 PM 9/7/2006, Lana Schaffer wrote: >Greetings, >I am wondering if it is recommended to reduce the input of gene list >from 45,000 genes >by some criteria before doing factor analysis with limma? > >Lana Schaffer >Biostatistics/Informatics >The Scripps Research Institute >DNA Array Core Facility >La Jolla, CA 92037 >(858) 784-2263 >(858) 784-2994 >schaffer at scripps.edu > > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111