Hi All, Is there a way to get the normalized log mean intensity values from the limma analysis, and then to rank order these values from 1 to 100? Thanks, Chuming

Hi Chuming, On 7/16/2012 9:25 AM, Chuming Chen wrote: > Hi All, > > Is there a way to get the normalized log mean intensity values from the limma analysis, and then to rank order these values from 1 to 100? It depends on what you mean by 'the normalized log mean intensity values'. After the lmFit() step, your MArrayLM object will have a coefficients list item (e.g., if you do fit <- lmFit(mydata), then fit$coefficients is what you want), which will contain all the estimated coefficients from your model fit. What those coefficients represent is dependent on how you specified your model, and what type of data you are using (single color or two-color data). So if you are using single-color data, and you fit a cell means model, and you normalized and took logs, then the coefficients will be the normalized log mean intensities for each sample type, by gene. And rank ordering of data is trivial - see the Introduction to R if you need help with that. Best, Jim > > Thanks, > > Chuming > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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