Hi all,

I have a question about multiple comparisons. 

The setup:

Let's say I have 3 groups and 1000 genes and I want to do all 3 possible
comparisons for every gene.

So I will have a matrix of 1000 rows and 3 columns with p-values.

I don't want to correct them all 3000 upon the time (would be too
conservative) therefore I use a say F statistic and get first a p-value
if is any difference 

between those groups for every gene. I correct the resulting 1000
p-values and decide to look at the all three comparisons only for the
genes whose F-statistic

p values was less than 0.05 after the correction, say there are 100 such
cases.

The question:

How should I correct the 3x100 individual p-values: a) by row, i.e. the
three p-values for one gene will be corrected upon the time or 

b) I consider them all together for all the genes and I correct a vector
of 300 p values.

 

I know a) will be less stringent than b) but I want to know which the
right one is.

 

 Thanks

Laurentiu Tarca  

 

 


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