Hello! I analize Affymetrix chips. There are two groups of transgenic and nontransgenic mice with 3 samples in each group. I normalised my data using rma, and calculated an adjusted p-value using multtest package. I have found out that there are about 64 differentially expressed genes between these two groups (alpha=0.01) (I used Bonferroni procedure). Next question is which of these genes are up- and down-regulated? How could I find out it? Thank you very much! [[alternative HTML version deleted]]

Assuming you were using a t-test, you could look at the sign (positive or negative) of the test from the multtest procedure. You could also look at the expression values themselves (very useful, as there are many instances where statistical significance may not be at all biologically interesting, and vice-versa). Sean On 5/20/04 7:13, "Vitalina Komashko" <vmkomashko@bionet.nsc.ru> wrote: > Hello! > I analize Affymetrix chips. There are two groups of transgenic and > nontransgenic mice with 3 samples in each group. I normalised my data using > rma, and calculated an adjusted p-value using multtest package. I have found > out that there are about 64 differentially expressed genes between these two > groups (alpha=0.01) (I used Bonferroni procedure). > Next question is which of these genes are up- and down-regulated? How could I > find out it? > Thank you very much! > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >