?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. ______________________________________________ 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.
