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. > > > > _______________________________________________ > > 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 > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 [[alternative HTML version deleted]]