Hi, I can see in the topTable documentation that "|toptable| is an earlier interface and is retained only for backward compatibility." However, if this is the case I would have thought I would get the same results with both methods. Instead this is what I get with topTable ID p.s.X.n.s.X t F P.Value adj.P.Val 10878 201429_s_at -0.10536776 14.17887 42456.21 5.325611e-29 9.481334e-26 18250 208834_x_at -0.01423163 14.00786 41650.35 6.079627e-29 9.481334e-26 22094 212788_x_at 0.01454676 14.20958 41614.89 6.115511e-29 9.481334e-26 18241 208825_x_at -0.02691777 14.00615 41546.70 6.185202e-29 9.481334e-26 and this is what I get using toptable logFC t P.Value adj.P.Val B 36960 13.278474 55.61688 1.183004e-17 6.468076e-13 28.81054 32762 9.208360 49.09926 6.570132e-17 1.284238e-12 27.66241 54191 10.949433 47.88478 9.270056e-17 1.284238e-12 27.41920 14250 7.630690 47.83800 9.395430e-17 1.284238e-12 27.40963 the p-values are different as are the columns provided. Is this right, and if so why is it the case? thanks, Sebastien

Sebastien. Yes, it is right. Have a look at the code for the two functions ... different defaults ... specifically with respect to what parameters those p-values (and t/F statistics) are calculated on. In fact, you'll notice that 'topTable' can call 'toptable'. M. On 16/01/2008, at 4:09 PM, Sebastien Gerega wrote: > Hi, > I can see in the topTable documentation that "|toptable| is an earlier > interface and is > retained only for backward compatibility." However, if this is the > case > I would have > thought I would get the same results with both methods. Instead > this is > what I get > with topTable > ID p.s.X.n.s.X t F P.Value > adj.P.Val > 10878 201429_s_at -0.10536776 14.17887 42456.21 5.325611e-29 > 9.481334e-26 > 18250 208834_x_at -0.01423163 14.00786 41650.35 6.079627e-29 > 9.481334e-26 > 22094 212788_x_at 0.01454676 14.20958 41614.89 6.115511e-29 > 9.481334e-26 > 18241 208825_x_at -0.02691777 14.00615 41546.70 6.185202e-29 > 9.481334e-26 > > and this is what I get using toptable > logFC t P.Value adj.P.Val B > 36960 13.278474 55.61688 1.183004e-17 6.468076e-13 28.81054 > 32762 9.208360 49.09926 6.570132e-17 1.284238e-12 27.66241 > 54191 10.949433 47.88478 9.270056e-17 1.284238e-12 27.41920 > 14250 7.630690 47.83800 9.395430e-17 1.284238e-12 27.40963 > > the p-values are different as are the columns provided. > Is this right, and if so why is it the case? > thanks, > Sebastien > > _______________________________________________ > 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