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(
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>
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.