Scale is written to do that IF you want to normalize according to the mean and the sd. For any other form of normalization, apply or sweep constructs will have to be used.
I couldn't really see a way of using the absolute median value in a sweep-statement. On Tue, May 25, 2010 at 7:11 PM, Bert Gunter <gunter.ber...@gene.com> wrote: > ?scale > > is specifically written for this. See also ?sweep > > Bert Gunter > Genentech Nonclinical Biostatistics > > > > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On > Behalf Of Joris Meys > Sent: Tuesday, May 25, 2010 9:54 AM > To: cobbler_squad > Cc: r-help@r-project.org > Subject: Re: [R] File normalization > > My code substracts the median absolute value. If you want to divide by it, > the code must be : > apply(some_dataset,2,function( > > > > x){ > > x/median(abs(x)) > > }) > > > Thanks to Peter Langfelder for pointing out my mistake. > > On Tue, May 25, 2010 at 6:24 PM, Joris Meys <jorism...@gmail.com> wrote: > > > What kind of normalization do you want to do? > > If you want to divide all columns by the median absolute value, try : > > > > apply(some_dataset,2,function(x){ > > x-median(abs(x)) > > }) > > > > also look at ?scale for normalization using the average and the sd. > > Cheers > > Joris > > > > > > On Tue, May 25, 2010 at 6:01 PM, cobbler_squad <la.f...@gmail.com> > wrote: > > > >> > >> Dear all, > >> > >> I have a file with 57 columns (671 time points in each column) > >> > >> File looks like this: > >> 1 0.279191 -1.203200e-02 -0.166772 6.12080e-02 0.196379 > >> 4.591900e-02 0.293689 > >> 2 0.267017 -1.150700e-02 -0.159463 5.85400e-02 0.187775 > >> 4.392200e-02 0.280854 > >> 3 0.053778 -2.322000e-03 -0.032103 1.18490e-02 0.037921 > >> 8.867000e-03 0.056571 > >> 4 0.035469 -1.531000e-03 -0.021166 7.79200e-03 0.024937 > >> 5.843000e-03 0.037273 > >> 5 0.040774 -1.761000e-03 -0.024342 8.96000e-03 0.028674 > >> 6.726000e-03 0.042910 > >> 6 -0.359709 1.547400e-02 0.214844 -7.87320e-02 -0.253034 > >> -5.905100e-02 -0.378322 > >> > >> I need to normalize it -- is it possible? > >> > >> I looked into normalize columns of a matrix to have the median absolute > >> value in R, but I am not sure how to apply it in this case. Would very > >> much > >> appreciate any input you could give me.. > >> > >> Thank you all in advance, > >> > >> Cobbler > >> -- > >> View this message in context: > >> http://r.789695.n4.nabble.com/File-normalization-tp2230251p2230251.html > >> Sent from the R help mailing list archive at Nabble.com. > >> > >> ______________________________________________ > >> R-help@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> PLEASE do read the posting guide > >> http://www.R-project.org/posting-guide.html > >> and provide commented, minimal, self-contained, reproducible code. > >> > > > > > > > > -- > > Joris Meys > > Statistical Consultant > > > > Ghent University > > Faculty of Bioscience Engineering > > Department of Applied mathematics, biometrics and process control > > > > Coupure Links 653 > > B-9000 Gent > > > > tel : +32 9 264 59 87 > > joris.m...@ugent.be > > ------------------------------- > > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php > > > > > > -- > Joris Meys > Statistical Consultant > > Ghent University > Faculty of Bioscience Engineering > Department of Applied mathematics, biometrics and process control > > Coupure Links 653 > B-9000 Gent > > tel : +32 9 264 59 87 > joris.m...@ugent.be > ------------------------------- > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
