[BioC] warning message from duplicateCorrelation in limma

[Gordon Smyth]

Is does not make sense to fit the same factor as both random (block) and 
fixed (in the design matrix), which is what you are doing. It doesn't make 
sense from a scientific, statistical or computing point of view.

You have two choices: (i) simply average the dye swaps and compute fold 
changes between treatments or (ii) use lmFit() with an apriori fixed 
correlation, e.g., around 0.3, which would be similar to (i) but would 
down-weight probes with disagreement between dye swaps. In the latter case, 
you should also include a dye-effect term.

Gordon

At 07:58 AM 18/05/2005, Na, Ren wrote:
>Dr. Smyth,
>
>If I want to use the argument block, the blocks in the pair should 
>correspond to biological replicates,
>but mine is not. So I can't use block. Is that what you mean.
>
>Yes, you are right. we don't have biological replicates. All samples are 
>extracted from cell culture dishes.
>
>Thanks!
>
>Ren