Hi Mark, On 10/27/2012 5:13 PM, Mark B wrote: > Hi, > I am trying to normalize a matrix of logged (base 2) cDNA expression > intensity values (dimensions 4000, 4) from only the Cy5 channel derrived > from an marrayraw object. I would like to normalize the values > using global median normalization where all arrays result having the same > median value. I would also like a matrix returned from the function. > > I have found how to use this normalize using an marrayraw object as > argument ( e.g. maNorm(m, norm="median") ) but > I can't seem to find how to do this with a matrix as argument. > > I have also tried the following but while my argument is a matrix my output > is a numeric vector that I can't seem to coerce > back into a matrix with the same dimensions I started with. > > > # median normalize all samples (columns) > > s.median<- apply(s, 2, median) > > class(s.median) > > [1] "numeric" Right. You calculated the median for each column of your matrix, which is what the apply() function is for (e.g., you apply a function over the margins of a matrix - the columns in your case). So what you really want here is the sweep() function, which is admittedly a bit cryptic (at least it was for me at one time). Anyway, the idea is that you will remove (sweep) a summary statistic over the margins of a matrix, based on a function you supply. The default is to subtract, which happens to be what you want to do. norm.mat <- sweep(s, 2, s.median) As an aside, single letter object names are fine for just playing around with data, but I would caution against using them for 'real' code. IMO it is advantageous to use a descriptive name for objects, so when you are looking back at your code in the future you don't have to go step by step to figure out what a and b and c and d and f are. Best, Jim > > > > Any hints? > > > > Thanks in advance, > > MAB > > [[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

Dear MAB, normalizeMedianValues() in the limma package does exactly this. Best wishes Gordon ------------ original message ---------------------- [BioC] medain global normalize - argument matrix Mark B mablfm at gmail.com Sat Oct 27 23:13:51 CEST 2012 Hi, I am trying to normalize a matrix of logged (base 2) cDNA expression intensity values (dimensions 4000, 4) from only the Cy5 channel derived from an marrayraw object. I would like to normalize the values using global median normalization where all arrays result having the same median value. I would also like a matrix returned from the function. I have found how to use this normalize using an marrayraw object as argument ( e.g. maNorm(m, norm="median") ) but I can't seem to find how to do this with a matrix as argument. I have also tried the following but while my argument is a matrix my output is a numeric vector that I can't seem to coerce back into a matrix with the same dimensions I started with. # median normalize all samples (columns) s.median <- apply(s, 2, median) class(s.median) [1] "numeric" Any hints? Thanks in advance, MAB ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}