[BioC] What does this P value column measures in LIMMA Time series analysis

James W. MacDonald jmacdon at med.umich.edu
Tue Nov 11 14:22:17 CET 2008

Hi Yemi,

yemi yomi wrote:
> Dear All, I carried out a time series analysis of a time course
> dataset using LIMMA method and I obtained a list of genes that change
> with time. However, I wonder if any one could explain in clearer
> terms what the P value column is measuring?
> The result output is as follows: ID, all Time contrasts(i.e
> Treatment-Controls), F, P value, adj.p value

Without giving us a simple example (see the posting guide) you leave us 
guessing as to what you have done. However, you might need to look at 
?topTable, specifically the 'coef' argument.



> Is the p value equals the average of all the contrast p values? In
> fact I am thinking of seeing each contrast(i.e. time point) with it
> own p value separately?
> Apologies for this rather naive questions. Yemi
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James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646

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