[BioC] Limma Coefficients using lmscFit
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)
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
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