I have the following expression data from test and control, each contain two sample. test <- c(3922.89022881,4235.76026274) control <- c(3694.11962861,4369.97835686) I want to compute P-value using , to see if they are differentially expressed, using "ebayes" http://rss.acs.unt.edu/Rdoc/library/limma/html/ebayes.html' What's the way to go about it? It's not clear from the help file. - G.V. [[alternative HTML version deleted]]

Hi Gundala, On 4/15/2013 10:11 PM, Gundala Viswanath wrote: > I have the following expression data > from test and control, each contain two sample. > > test<- c(3922.89022881,4235.76026274) > control<- c(3694.11962861,4369.97835686) > > > I want to compute P-value using , to see if > they are differentially expressed, using > "ebayes" http://rss.acs.unt.edu/Rdoc/library/limma/html/ebayes.html' > > What's the way to go about it? > It's not clear from the help file. You wouldn't use eBayes() for making a single comparison. And you wouldn't normally use unlogged data. And just looking at those data, I can tell you the p-value is going to be very close to 1. Best, Jim > > > > - G.V. > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

eBayes() is for use with microarray data, i.e. when you are measuring the expression of many genes, as it works by borrowing information across all genes. If you are measuring the expression of just one gene (assuming the measurement wasn't derived from a microarray), you should use a t.test(). Paul. On Tue, Apr 16, 2013 at 3:11 AM, Gundala Viswanath <gundalav at="" gmail.com=""> wrote: > I have the following expression data > from test and control, each contain two sample. > > test <- c(3922.89022881,4235.76026274) > control <- c(3694.11962861,4369.97835686) > > > I want to compute P-value using , to see if > they are differentially expressed, using > "ebayes" http://rss.acs.unt.edu/Rdoc/library/limma/html/ebayes.html' > > What's the way to go about it? > It's not clear from the help file. > > > > - G.V. > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Dr. Paul Geeleher, PhD (Bioinformatics) Section of Hematology-Oncology Department of Medicine The University of Chicago 900 E. 57th St., KCBD, Room 7144 Chicago, IL 60637 -- www.bioinformaticstutorials.com