[BioC] (Limma) different toptable results for the same dataset using 2 different designs

[Gordon Smyth]

At 10:37 PM 6/12/2005, Celine Carret wrote:
>Dear gordon, thank you very much for your answer.
>However, when I do that, I end up with the table below:

[code deleted]

>             M          t   P.Value          B
>>311  -3.997113 -13.961019 0.5794648 -0.5112598
>>1327 -1.461801 -11.334987 0.5794648 -0.6889117
>>113  -1.690073 -10.880814 0.5794648 -0.7308602
>>4408 -3.066882 -10.019535 0.5794648 -0.8232774
>>1825 -3.576034  -9.781223 0.5794648 -0.8523026
>>1224 -1.099785  -9.445264 0.5794648 -0.8961448
>>289  -2.800736  -9.306995 0.5794648 -0.9152559
>>288  -1.689312  -8.759499 0.5794648 -0.9977157
>>2892 -2.513426  -8.675603 0.5794648 -1.0113879
>>3311  3.005392   8.377018 0.5794648 -1.0625077

This isn't a surprise. Your previous email showed that this is the table 
you must get.

>It does solve one problem, which is obatining 2 similar toptables whatever 
>the design lay-out, but it doesn't explain why I have those awfully wrong 
>values...
>Would have an idea by any chance?
>
>All the best,
>Celine

If you claim the answers are wrong, you rather do need to give a reason why 
you think that.

Best wishes
Gordon