


Hi
Gordon,

Thanks for your suggestion. That helped a lot!



I had one more question: if the patient to patient variability is too large,
would you recommend doing a Welch's t-test? Is there a way to do it in limma
using the same linear model (~patient + dis + dis:tx)?



Thanks,

Som.



> Date: Wed, 4 Jul 2012 10:27:18 +1000
> From: smyth@wehi.EDU.AU
> To: genome1976@hotmail.com
> CC: bioconductor@r-project.org; maintainer@bioconductor.org
> Subject: Re: LIMMA paired T-test
> 
> Your design matrix is not sufficient to answer questions 2 and 3.  Your 
> questions presume an interaction between treatment and disease, i.e., 
> distinct effects for treatment for disease and healthy, whereas your model 
> formula assumes no interaction.
> 
> You need:
> 
>    design <- model.matrix(~patient + dis + dis:tx)
> 
> Then last two coefficients answer questions 2 and 3.
> 
> Gordon
> 
> ---------------------------------------------
> Professor Gordon K Smyth,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> http://www.wehi.edu.au
> http://www.statsci.org/smyth
> 
> On Tue, 3 Jul 2012, somnath bandyopadhyay wrote:
> 
> >
> > Hi Gordon and LIMMA users,
> >
> > I am sure this question has been answered before and I tried looking into the archives for some answer but did n't have any success there.
> >
> > My experimental design has diseased and healthy volunteers blood treated with a drug. I have gene expression data for both before and after treatment. So, I have disease, treatment and patient_ID (before vs. after treatment) as covariates. What I am interested in are as follows:
> >
> > 1. What genes change in untreated disease vs. untreated healthy volunteers?
> > 2. What genes change in treated disease vs. untreated disease blood samples?
> > 3. What genes change in treated healthy volunteers vs. untreated healthy volunteers blood samples?
> >
> > Design of the experiment:
> > design <- model.matrix(~ dis + tx + patient)
> >
> > Based on the above design I am able to answer question 1. I was 
> > wondering how I would answer question 2 and 3 in a paired T -test (to 
> > account for before vs. after treatment). Do I need to do some contrasts 
> > because I have been trying to work off the lmfit.
> >
> > Any help would be greatly apreciated.
> >
> > Thanks,
> > Som.
> >
> >
> >
> >
> >
> 
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:9}}

