[R] File normalization

[Bert Gunter]

?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

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