[BioC] limma user's guide example

[Giovanni Coppola]

Hi Naomi and Jim,
thanks for your replies.
I agree that genes and p-values will stay the same.
However, for this particular example, two possible approaches are  
presented, and - as they stand now - they are conflicting, yielding  
results with opposite signs.
Best
Giovanni


On Oct 4, 2006, at 1:19 PM, Naomi Altman wrote:

> You can do it either way and you will obtain the same p-values.  Of  
> course, the sign of M will be reversed.
>
>
> --Naomi
>
> At 03:58 PM 10/4/2006, Giovanni Coppola wrote:
>> Sorry guys, another DQ (dumb question)....
>> Limma User's Guide pag. 39 and 42, line:
>> cont.matrix <- makeContrasts(MUvsWT=WT-MU, levels=design)
>> Why not MU-WT?
>> Thanks
>> Giovanni
>>
>>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> 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
>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348  
> (Statistics)
> University Park, PA 16802-2111
>