Thanks for this info. I will try it ou. Regards. Stephen. On Mon, 2003-08-18 at 23:33, Rafael A. Irizarry wrote: > if you are using affy, the typical thing to do is normalize the probe > level data. if you have probe level data in an AffyBatch object you can > use the normalize method and decide on the normalization approach via the > "method" argument. > the vignetts for the affy package have much more info. i dont think > normalize will work on matrix. > > the different methods have "engine" functions that work on matrices so if > you want to normalize data on a matrix you can do this as well but you > need to call functions other than "normalize", for example > normalize.quantiles, normalize.qsplines. in general normalize.methodname. > look at the help file for normalize. > > notice that by default the functions mas5, rma, and justRMA do the > normalization as part as the reduction of probe level data to expression > summaries. > > -r > > On Mon, 18 Aug 2003, Stephen Nyangoma wrote: > > > Hi Rafael, > > Sorry, I have just used > > normalize.quantiles(mydata) and seems to have worked (given me > > something). But wanted to use the > > normalize() object. Does this work differently? Where can I get more > > information on how each normalization method works. My aim is to use a > > variety of methods to explore this data set. > > > > I am using library(affy). > > > > Regards. Stephen. > > > > > > > > On Mon, 2003-08-18 at 22:56, Rafael A. Irizarry wrote: > > > what kind of object is Data8pm? normalize doesnt work on any R object. > > > plus different types of ata are nornalized differentily. > > > > > > > > > On Mon, 18 Aug 2003, Stephen Nyangoma wrote: > > > > > > > > > > > Hi All, > > > > Am trying to normalize a data set and obtaining the following error > > > > > > > > > load("Data8pm.Rdata") > > > > > normalize(Data8pm) > > > > Error in normalize(Data8pm) : No direct or inherited method for function > > > > "normalize" for this call > > > > > > > > > > > > > Can some one please, advise on the mistake I am making? > > > > > > > > Thanks for your help. > > > > > > > > Stephen. > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@stat.math.ethz.ch > > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor