I Hi, I am using R and tried to normalize the data within each sample group using RMA. When I tried to import the all the normalized expression data as a single text file and make a boxplot, it showed discrepancy among the sample groups. I tried to scale them or re-normalize them again, so that it can be used for further analysis. Would you please help me out with this problem. -- Hossain Nawaz,MD Karolinska Institutet Clinical Research Center [[alternative HTML version deleted]]

On Mon, Oct 18, 2010 at 4:42 AM, Hossain Nawaz <hmnawaz@gmail.com> wrote: > I Hi, > > I am using R and tried to normalize the data within each sample group using > RMA. When I tried to import the all the normalized expression data as a > single text file and make a boxplot, it showed discrepancy among the > sample > > groups. I tried to scale them or re-normalize them again, so that it can > be > used for further analysis. Would you please help me out with this problem. > > > Hi, Hossain. You should normalize all the samples together, not separately. There are numerous posts in the mailing list archives on how to accomplish this with largish data sets. Sean [[alternative HTML version deleted]]