File normalization
The scale function can use whatever vector you choose for subtraction and division. (It's basically a wrapper for the sweep function.) For example, to subtract the median and divide by the median absolute deviation, use scale(x,center=apply(x,2,median),scale=apply(x,2,mad)) Either the center= or scale= arguments can be omitted if you only want to divide or subtract. - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spector at stat.berkeley.edu
On Tue, 25 May 2010, Joris Meys wrote:
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.berton at gene.com> wrote:
?scale is specifically written for this. See also ?sweep Bert Gunter Genentech Nonclinical Biostatistics -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Joris Meys Sent: Tuesday, May 25, 2010 9:54 AM To: cobbler_squad Cc: r-help at 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 <jorismeys at 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.foma at 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.
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-- 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.Meys at 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.Meys at Ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]]
______________________________________________ R-help at 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.Meys at Ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]]
______________________________________________ R-help at 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.