lme question

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lme question

Mahdi Osman
Hi list,


I am fitting microarray data (intensity) model using the lme package in R
environment. I have 5 fixed variables in the model. One of the fixed
variables is genes. I am trying to get p-values for  different genes. But I
am getting only one p-value for all genes together. I can get a list of
p-value when I run lm. Why can't this work in lme?


I was wondering if some one can help me solve this problem. That is getting
a list of p-value for each gene in the model using the lme.


Thanks in advance for your help


Regards



Mahdi

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Re: lme question

Dieter Menne
Mahdi Osman <m_osm <at> gmx.net> writes:

>
> Hi list,
>
> I am fitting microarray data (intensity) model using the lme package in R
> environment. I have 5 fixed variables in the model. One of the fixed
> variables is genes. I am trying to get p-values for  different genes. But I
> am getting only one p-value for all genes together. I can get a list of
> p-value when I run lm. Why can't this work in lme?
>
> I was wondering if some one can help me solve this problem. That is getting
> a list of p-value for each gene in the model using the lme.
>

The bioconductor list might be a better place for this question, and an example
would haven been welcome. So my only guess is: could it be that  you forgot to
make genes a factor variable? When genes is a number, you get a linear
regression which is probably not what you want.


Dieter

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