My suggestions to look into CMA, glmnet, huge, PMA, and the like, remain :-)

Anyone used the 'survcomp' package?  It seems handy for a number of purposes
and comes with a particularly nice, contrarian vignette :-D


On Sat, Jul 9, 2011 at 2:51 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> Dear Bonnie,
>
> The issue isn't so much between linear and logistic regression, as between
> differential expression (in the outcome is used to explain expression, as in
> limma) and prediction (in which expression is used to explain the outcome).
>
> I don't work in the prediction and can't recommend packages.
>
> Best wishes
> Gordon
>
> ------------------------------**---------------
> Professor Gordon K Smyth,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> smyth@wehi.edu.au
> http://www.wehi.edu.au
> http://www.statsci.org/smyth
>
>
> On Sat, 9 Jul 2011, Joubert, Bonnie (NIH/NIEHS) [E] wrote:
>
>  I have a related question to limma .  I would like to run a logistic model
>> with my data where I have a dichotomous outcome and the predictor variables
>> are the methylation values (exprs(mldat)).  LmFit is for a linear model
>> only.  Is there a related package for performing logistic regression?
>>
>> Thanks,
>> Bonnie
>>
>
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