[BioC] Paired samples and origin question, Limma

[Gerhard Thallinger]

Hello Morton,

>> ...
>> I want to correct for the variance introduced by the different 
>> labs and biological differences from the repsective patients.  
>> As I understand it I can use the block option in lmFit to 
>> correct for this.
>> 
>> Do the following Limma code correct for the origin of the samples, 
>> and how can I add information that the samples are paired by patients ?

> ...
> In your case, you have two blocking variables (lab and patient), so 
> you are going to have to handle the patient pairing by hand. 

  Based on Gordons reply to a similar question, limma should be
  able to handle it: lab with blocking and patient as a fixed effect:

    https://stat.ethz.ch/pipermail/bioconductor/2005-March/007864.html   

Regards

Gerhard