Dear all, Newbie Here, I have a matrix a data with genes in rows and sample in columns. # express is my expression matrix normalize.invariantset (expres, as.matrix (apply(expres,1,mean))) #gives Error in while ((ns.old - ns) > 50) { : missing value where TRUE/FALSE needed What should I do?

Hi Ali, On 3/4/2012 5:28 AM, Ali Mohammadian wrote: > Dear all, > > Newbie Here, > > I have a matrix a data with genes in rows and sample in columns. > > # express is my expression matrix > normalize.invariantset (expres, as.matrix (apply(expres,1,mean))) > #gives > Error in while ((ns.old - ns)> 50) { : > missing value where TRUE/FALSE needed > > What should I do? Since you are a newbie, I won't just say RTFM. However, that is really what you should do. From ?normalize.invariantset: Arguments: abatch: an AffyBatch object. data: a vector of intensities on a chip (to normalize to the reference). ref: a vector of reference intensities. prd.td: cutoff parameter (details in the bibliographic reference). baseline.type: specifies how to determine the baseline array. type: a string specifying how the normalization should be applied. See details for more. verbose: logical indicating printing throughout the normalization. You are using positional arguments, so the two values you are passing in should be 1) An AffyBatch object. 2) A vector of intensities. What you are passing in to this function appears to be neither, so getting an error isn't that surprising. Perhaps you could say more about what you are trying to do, as passing an expression matrix to normalize.invariantset() doesn't make sense. Best, Jim > > _______________________________________________ > 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