[R] mixed model for analysing microarray data

[Jack]

Dear R users, 

We are trying to analyse microarray data. The experiment compares two conditions (light vs. dark). we would like to use a mixed-model ANOVA but we don't know much about it. could you please help?
the experiment test the effect of light on a tissue and compare tissues maintained in light or dark (fixed effect).
In each condition, Two RNA samples were used (random effect?) for each condition, and each sample was measured twice (random effect? nested in sample?), or maybe the replicate factor is not required?

Any help will be appreciated (particularly on how to assign the random factor(s) )

for a given gene the data look like that:

light  RNA  replicate  reading
"y"     1     1          1.67
"y"     1     2          1.56
"y"     2     1          1.60
"y"     2     2          1.34
"n"     1     1          1.67
"n"     1     2          1.56
"n"     2     1          1.60
"n"     2     2          1.34




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