Hi, I'm trying to normalize a table of probe level intensities (pls. see attachment). Would you recommend a method, which would take only a matrix but not an AffyBatch or object and do quantile normalization, in R/Bioconductor packages. I came across normalize.quantiles {affy} but got the following errors: ------ > library(affy) > normalize.quantiles(intensity.M,copy=TRUE) Error: could not find function "normalize.quantiles" ------ Thanks, Dorothy -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: input.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100727="" 09eb5766="" attachment-0001.txt=""> -------------- next part --------------

Hi, On Tue, Jul 27, 2010 at 7:19 PM, dorothyc <dorothyc at="" bcgsc.ca=""> wrote: > Hi, > > I'm trying to normalize a table of probe level intensities (pls. see attachment). ?Would you recommend a method, which would take only a matrix but not an AffyBatch or object and do quantile normalization, in R/Bioconductor packages. > > I came across normalize.quantiles {affy} but got the following errors: > ------ >> library(affy) >> normalize.quantiles(intensity.M,copy=TRUE) > Error: could not find function "normalize.quantiles" > ------ How about: R> library(limma) R> normalizeBetweenArrays(intensity.M, method='quantile') > > Thanks, > Dorothy > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

By the way .. On Tue, Jul 27, 2010 at 7:19 PM, dorothyc <dorothyc at="" bcgsc.ca=""> wrote: > I came across normalize.quantiles {affy} but got the following errors: > ------ >> library(affy) >> normalize.quantiles(intensity.M,copy=TRUE) > Error: could not find function "normalize.quantiles" > ------ normalize.quantiles is in the preprocessCore library: R> library(preprocessCore) R> normalize.quantiles(...) -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact