Hi, >From my best understanding, Sean is generally correct...but depending on your experimental design you may consider using the Ebarrays package, which would allow you to make some probabilistic statements. Cheers, Rick On 20/12/10 6:25 PM, "Sean Davis" <sdavis2 at="" mail.nih.gov=""> wrote: > On Mon, Dec 13, 2010 at 5:55 PM, Li, Aiguo (NIH/NCI) [E] > <liai at="" mail.nih.gov="">wrote: > >> Thanks, Jim. >> >> One more question related to p value >> >> I need to generate a fold changes based on only 2 arrays; I like to get a >> p values associated with fold changes. Which package in R allow me to do >> this? >> >> > The best you can do is fold change with only two arrays. Just rank your > genes by fold change and talk to the experimentalists about getting some > replicates. It isn't really possible or even meaningful to talk about > p-values with only two arrays. > > Sean > > > >> Thanks, >> >> AG >> >> >> On 12/13/10 1:39 PM, "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: >> >> Hi AG, >> >> On 12/10/2010 10:25 AM, Li, Aiguo (NIH/NCI) [E] wrote: >>> Hi all, >>> >>> I want to get a probeset level data set without mas5 normalization and >> used the following script. Could someone tell me this is right or not? >>> >> >> Yes. >> >> Best, >> >> Jim >> >> >>> affydata<- ReadAffy() >>> ExprNonorm<-mas5(affydata,normalize=F) >>> >>> Does these script do the background correction? Or only summarize the >> probeset level data? >>> >>> Thanks, >>> >>> AG >>> >>> _______________________________________________ >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> >> _______________________________________________ >> 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 >> > > [[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 -- Rick Frausto PhD Candidate The University of Sydney School of Molecular Bioscience G08 Camperdown, NSW 2006 AUSTRALIA ricardo.frausto at sydney.edu.au Phone: 61 2 9036 5354 Lab of Iain L. Campbell