Sorry for the incomplete message, click the send accidentally. This analysis is for only one group of 4 biological replicates such as: group array1 a array2 a array3 a array4 a I tried to identify the genes which are differently expressed in group a, but no other reference groups for comparison. Therefore, even all the t statistics are positive. Any thoughts? Thanks. On Tue, Sep 15, 2009 at 11:13 AM, zrl wrote: > Hi Heidi, > > Thank you for your response. Maybe I didn't make my question very clear. > This analysis is for only one group of 4 biological replicates such as: > group > array1 > > > > > On Tue, Sep 15, 2009 at 4:20 AM, Heidi Dvinge wrote: > >> Hello, >> you can just sort the topTable result by the t-statistics since these will >> be either positive or negative, or call it directly with sort.by="t" and >> then filter for significant p-values. >> >> HTH >> \Heidi >> >> On 15 Sep 2009, at 10:05, zrl wrote: >> >> Dear List, >> >> I have several biological replicates affy arrayes (a simple one group 4 >> arrayes), and tried to use eBayes to get the differentially expressed >> genes. >> The topTable ranked the genes by B statistics, which mixed over-expressed >> genes and under-expressed genes. My question is how I should separate the >> over and under expressed genes from topTable results. My idea is to >> calculate the mean average expressed value/intensities (extracted from >> topTable results with using the number of all the genes) and compare >> ranked >> genes with the mean value, if the expressed value is greater than the >> mean, >> I take this gene as over-expressed, otherwise, it's under-expressed. >> Since I don't know the underlying implement of topTable or eBayes, I want >> to >> make sure if my method is right. Or you have some better ideas. Thanks. >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > [[alternative HTML version deleted]]