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
spec...@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.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
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PLEASE do read the posting guide
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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.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.
______________________________________________
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.
