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 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

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. Best, Jim > > 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 > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662