Hi Jim,
 
Thank you very much for your reply. I got what you  mean. Yes, I am doing comparisons between groups (subjects)and I will go ahead with limma.
 
Best,
Zhengyu 
 
> Date: Tue, 10 Dec 2013 09:04:48 -0500
> From: jmacdon@uw.edu
> To: guest@bioconductor.org
> CC: bioconductor@r-project.org; zhyjiang2006@hotmail.com
> Subject: Re: [BioC] Apply non-Gaussian distribution data to limma
> 
> Hi Jiang,
> 
> The distributions you are talking about are within subject (e.g., the 
> distribution of the expression values for multiple genes from an 
> individual), but the comparisons you are making are between subjects.
> 
> It really doesn't matter what the within subject distributions look 
> like, unless you are concerned with intra-subject comparisons. The 
> between subject comparisons are usually based on far too few replicates 
> to get a real sense of the distribution, and you are usually making 
> thousands of such comparisons, so even if you could check the gene-wise 
> distributions you would then have to 'fix' them one by one.
> 
> Luckily, the t-statistic is pretty robust to non-normal distributed 
> data, so you (like thousands of people already) can just go ahead and 
> fit the model using limma. If you are really worried, you could use a 
> resistant regression but the cost is power, which most microarray 
> studies (at least in my experience) are lacking already.
> 
> Best,
> 
> Jim
> 
> 
> 
> On Monday, December 09, 2013 10:02:25 PM, Jiang [guest] wrote:
> >
> > Hi,
> > I have high through array data with two peaks in its distribution (raw and log 2 transformed). I googled it looks like is mixed Gaussian distribution - two normal distribution as some people suggested. I think limma's assumption is normal distribution. I was wondering if there is any way to fix the problem or to convert my data to normal distribution before applying to limma.
> >
> > Thanks,
> > Jiang
> >
> >   -- output of sessionInfo():
> >
> > see question
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
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> 
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
 		 	   		  
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