[BioC] single channel analysis of loop designs

Naomi Altman naomi at stat.psu.edu
Wed Jan 4 02:25:45 CET 2006

Dear Matthew,
I guess the main publication is my own - at present only an 
unrefereed conference proceeding. 
  I think that the Kerr and Churchill papers do it this way, too, but 
they do not explain why.

Basically, using differences has 2 disadvantages - it has higher 
variance than single channel analysis, and if a spot is missing on an 
array, many of the effects for that gene cannot be estimated.

At 04:07 PM 1/3/2006, you wrote:
>Dear Naomi,
>I recently read a post of yours on the bioconductor listserv that 
>said you were a "big believer in single channel analysis of loop 
>designs." Can you point me towards any publications that sway your 
>opinion that way? I've always done dual channel analysis of loop 
>designs and never really thought much about the distinction.
>Thanks in advance for your help.
>Matt Scholz
>Senior Research Specialist
>Department of Plant Sciences
>University of Arizona
>(520) 621-1695

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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