R help - Feb 2010 - Can not p.adjust on the conservative analysis.

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