At 01:29 AM 31/05/2005, weinong han wrote: >thanks much for your help and explanations. > >Sure, I have run limma and computed moderated t statistics on 12 samples >in one group and >only 1 in the other. please see attached R script for my dat analysis and >QQ_plot. >QQ plot looks like somewhat abnormal, how to fix it ?any suggestions wil >be much appreciated. The QQ plot of t-statistics is only supposed to look normal when there is no differential expression. Deviations fro the line are supposed to indicated differential expression. >How about the results of moderated t statistics on 12 samples? how to get >the full list of significanly differentially expressed genes when setting >arbitrary p value cut off less than 0.05? results <- decideTests(fit, adjust="fdr", p=0.05) To select all up genes: fit.up <- fit[results[,2] ==1, ] To select all down genes: fit.down <- fit[results[,2]== -1, ] To output to a file: write.fit(fit.up[,2], file="myresults.txt") or simply write(fit.up[,2], file="myresults.txt") Gordon >thanks again. > >Best Regards