R help - Apr 2010 - model set up question

I need to compare gene expression differences between multiple line pairs of
alcohol preferring and non-preferring rat lines. I have 5 such line pairs, 3
are unrelated but two were derived independently from the same parent stock.
For each line, there are 10 samples. I'll be testing multiple genes, but for
simplicity assume just one gene whose expression is measures as
geneExpression.

Alcohol Preferring     Alcohol Non-Preferring     Line Pair         X or
Non-X

Line 1a                              Line 1b
1                     Non-X
Line 2a                              Line 2b
2                     Non-X
Line 3a                              Line 3b
3                     Non-X
Line X4a                            Line X4b
X4                   X
Line X5a                            Line X5b
X5                   X

If all the line pairs were independently derived, a model could be
geneExpression ~ Line.Pair + AlcoholPreference   with the factor of interest
being Alcohol Preference

but, there is the "X" factor, with the 2 "X strain-pairs being
related,
whereas the others are unrelated to each other and also to the 2 "X"
strain-pairs.

We want to take into account the fact that there are really only 4 parent
populations of these 5 strain-pairs so as to decrease the weighting put on
the "X" strains in the model.

What would the most appropriate approach to this be and how would the model
be written?

Thanks,

Mark

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

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