Please recognize that the following is by no means authoritative.  That
said, nobody else was providing an answer (perhaps for good reason!), so...

A typical workflow (if you've got candidate loci, say, 'gene1' and 'gene2'
calls, along with some other genotyped loci that you don't particularly care
about):

# y is a binary response, e.g. unaffected=0, affected=1
> y = your.outcomes

# we assume there will usually be population stratification;
# attempt to control for it using principal components of X
> library(pcaMethods)
> PCs = nipalsPca(t(your.data), nPcs=3) # can tolerate NAs

# I'm happy if max(R2cum) > 0.8; if not, set nPcs higher
> PCs@R2cum
[1] 0.8977354 0.9925331 1.0000000
> rsv = PCs@scores
> colnames(rsv) = paste('PC', 1:3, sep='')
> your.data = cbind(y, your.data, rsv)

# fit a logistic model w/main effects and an interaction,
# controlling (somewhat) for stratification (...maybe)
> fit = with(your.data,
             glm( y ~ gene1*gene2 + PC1 + PC2 + PC3,
                 family='binomial'))

# see what it tells you
> summary(fit)

# nb. if you had parent-child trios, you could instead use
# conditional logistic regression to emulate a TDT or FBAT

Hopefully you have candidate loci, because otherwise the simplistic exercise
above will be replaced by an entirely different kettle of fish if you don't.
 But then you should work with someone who does this stuff for a living and
not just randomly solicited, possibly untrustworthy advice from the
Interwebs.

IMHO, of course.

--t


2011/7/23 Simon Noël <simon.noel.2@ulaval.ca>

>
>   Hi,
>
>
>
>   I have some kind of a shameful question...  My director say that I will
> need
>   to do a logistic regression in order to test for gene-gene interaction...
>   But what's    that?     I tryed    to search    for   a   package that
>   do logistic regression on bioconductor and I get around 40 hit...  Witch
>   one should I use?
>
>
>   Simon NoÃ«l
>   CdeC
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
If people do not believe that mathematics is simple, it is only because they
do not realize how complicated life is.
John von Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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