Dear colleages, I can not uderstand a result I have. I made t-permutations and LIMMA to find differentially expressed genes on the same dataset. Is it posible I can have a gene which is overexpressed using t-permutations (t value = + something) and underespressed using LIMMA (Statistic= - something) ? Sorry but I can not fully understand the LIMMA algorithm yet. Many thanks, Francisco ___________________________________________ Fco. Javier Burguillo Departamento de Qu?mica F?sica Facultad de Farmacia Universidad de Salamanca Espa?a http://simfit.usal.es

Hi Francisco, Francisco Javier Burguillo wrote: > Dear colleages, > > I can not uderstand a result I have. I made t-permutations and LIMMA to > find differentially expressed genes on the same dataset. Is it posible I > can have > a gene which is overexpressed using t-permutations (t value = + something) > and underespressed using LIMMA (Statistic= - something) ? That's highly unlikely - the numerator (which is responsible for the sign of the statistic) is identical in both cases. The only differences are slight changes in how the denominator is computed, and what distribution the t-statistics are compared against. It's more likely that you have e.g. experimental - control in one case and control - experimental in the other. However, without seeing your code that's just a guess. Best, Jim > > Sorry but I can not fully understand the LIMMA algorithm yet. > > Many thanks, > > Francisco > > > > ___________________________________________ > Fco. Javier Burguillo > Departamento de Qu?mica F?sica > Facultad de Farmacia > Universidad de Salamanca > Espa?a > http://simfit.usal.es > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826