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RE: st: ANOVA Posthocs
From
"Feiveson, Alan H. (JSC-SK311)" <[email protected]>
To
"[email protected]" <[email protected]>
Subject
RE: st: ANOVA Posthocs
Date
Fri, 22 Oct 2010 15:41:04 -0500
SO this brings to mind the question:
Is it better (more powerful?) (or more correct?) to do 6 separate FDR analyses with 40 genes each using Scheffe or Tukey adjusted p-values for each gene, or one FDR analysis on 240 unadjusted t-test p-values?
Al Feiveson
-----Original Message-----
From: [email protected] [mailto:[email protected]] On Behalf Of Airey, David C
Sent: Friday, October 22, 2010 2:52 PM
To: [email protected]
Subject: re: st: ANOVA Posthocs
.
Maybe if you are doing 40*6=240 pairwise comparisons, do you want to consider controlling the false discovery rate? Along these lines, if you are doing oneway ANOVAs, why not use -regress- with the -test- command (http://www.stata.com/support/faqs/stat/test1.html) and -post- to file as you run through the genes and then submit the p-values to one of Roger Newson's packages like -smileplot or -qqvalue-?
> Greetings Statalisters.
>
> I am working on a multiple comparison problem comparing Y by Group with 4 groups, but I have MULTIPLE Y's that I need to consider because my Y's represent fold-increases in gene expression data and I'm working with over 40 genes...
>
> So in this effort, I'd like to run Oneway ANOVAs of Y by Group for each of my genes, capture the Pairwise comparisons among my groups into a separate dataset, and repeat this with a loop for each of the genes of interest.
>
> Ideally I'd like to use the Tukey-Kramer Pairwise user-written command (thanks Phil Enders), however that does not provide p-values in the screen output or any matrix in the return list.
>
> An alternative would be to use the Scheffe posthoc option to -oneway- but I can't figure out how to steal those p-values either?
>
> Any thoughts on how to grab these p-values?
> Much appreciated...
> Rob
>
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