HI, I am trying to quantile normalize my Agilent MiRNA array data. I have been following some instructions that should have worked: i have performed > read.table(), then corrected my data for Negative values then >Log2() transformed. My instructions were to then load the (affy) package then do: > normalize.quantiles(as.matrix(log2_file_name)) but there does not seem to be a normalize.quantiles() function. I am running R 2.8.0 with affy_1.20.0. Was this function from a previous version of affy or am i doing something stupid regards Matt (doesn't really know what he is doing) Nev

This was asked on the list the other day/week. normalize.quantiles() is now in 'preprocessCore'. /Henrik On Tue, Nov 11, 2008 at 2:45 PM, Matthew Neville <matthew.neville at="" oxlip.ox.ac.uk=""> wrote: > HI, > > I am trying to quantile normalize my Agilent MiRNA array data. > > I have been following some instructions that should have worked: > > i have performed > read.table(), then corrected my data for Negative values > then >Log2() transformed. > > My instructions were to then load the (affy) package then do: > >> normalize.quantiles(as.matrix(log2_file_name)) > > but there does not seem to be a normalize.quantiles() function. > > I am running R 2.8.0 with affy_1.20.0. Was this function from a previous > version of affy or am i doing something stupid > > regards > > Matt (doesn't really know what he is doing) Nev > > _______________________________________________ > 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 >