Hi Chad, There are not many significant transcript clusters after p.adjust.
> sum(adjusted_pvalue[,'C-D']<.05) [1] 0 > sum(adjusted_pvalue[,'A-D']<.05) [1] 0 > sum(adjusted_pvalue[,'D-E']<.05) [1] 2 > sum(adjusted_pvalue[,'A-B']<.05) [1] 8 However, there are may TCs that are significant before p.adjust. Which one we should use? > sum(pvalue_table[,'C-D']<.05) [1] 1371 > sum(pvalue_table[,'A-D']<.05) [1] 903 > sum(pvalue_table[,'D-E']<.05) [1] 982 > sum(pvalue_table[,'A-B']<.05) [1] 1964 I'm upstairs. Let me know when you have time. Regards, Peng ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
