[BioC] Limma Coefficients using lmscFit

Naomi Altman naomi at stat.psu.edu
Wed Dec 21 03:12:24 CET 2005

Being a big believer in single-channel analysis of loop designs, I 
used lmscFit to analyze my loop design data. All went well until the 
investigator requested the normalized single channel data.
Since lmscFit actually operates on M and A, we took the same MAlist, 
and created R and G using RG.MA.

To check the computation, we then computed the treatment means by 
hand for a few genes.  These did not work out to the same treatment 
means obtained from lmscFit (using model ~-1+Trt).

I hope that someone can explain why these are not equal.  (And I 
really hope that this is not another case where I did not read the 
documentation sufficiently carefully.)

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

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