R help - Jul 2006 - Find peaks in histograms / Analysis of cumulative frequency

Hello all,

I have some histograms of amount of DNA in some cells (DU145 cells
overexpressing Bax and Bcl-xL for those who wish to know). The histograms
show not only two peaks as expected, but three, indicating that some cells
have more than normal amounts of DNA.

I am interested in knowing how much of the cell populations are in each peak
as well as between.

I am not really sure how to go about it; I have been considering fitting a
gaussian distribution to each peak and integrate the part between the peaks
as described by Watson et al (1987 Cytometry 8:1-8). A more straight forward
and more visual approach appears to be plotting the cumulative frequencies.
In either case, I should like to find the peaks in the histogram
automatically, as well as getting proper information about the peaks.

How would I go about finding peaks using R? Also I have really not been able
to figure out how to fit a distribution.

Is there a way to analyse the cumulative frequencies? the knots() function
appears to return far too many knots.

I am relatively new to R, but do have good programming experience, though I
am mostly biologist.

Thank you in advance for any inputs.

PS. An example of the histogram can be found
here<http://photos1.blogger.com/blogger/7029/2724/1600/DU145-Bax3-Bcl-xL.png>

	[[alternative HTML version deleted]]

Hi

There are some mail archives about peaks
eg.
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/33097.html 

HTH
Petr



On 15 Jul 2006 at 13:55, Ulrik Stervbo wrote:

Date sent:      	Sat, 15 Jul 2006 13:55:26 +0200
From:           	"Ulrik Stervbo" <ulriks at ruc.dk>
To:             	r-help at stat.math.ethz.ch
Subject:        	[R] Find peaks in histograms / Analysis of cumulative frequency
> Hello all,
> 
> I have some histograms of amount of DNA in some cells (DU145 cells
> overexpressing Bax and Bcl-xL for those who wish to know). The
> histograms show not only two peaks as expected, but three, indicating
> that some cells have more than normal amounts of DNA.
> 
> I am interested in knowing how much of the cell populations are in
> each peak as well as between.
> 
> I am not really sure how to go about it; I have been considering
> fitting a gaussian distribution to each peak and integrate the part
> between the peaks as described by Watson et al (1987 Cytometry 8:1-8).
> A more straight forward and more visual approach appears to be
> plotting the cumulative frequencies. In either case, I should like to
> find the peaks in the histogram automatically, as well as getting
> proper information about the peaks.
> 
> How would I go about finding peaks using R? Also I have really not
> been able to figure out how to fit a distribution.
> 
> Is there a way to analyse the cumulative frequencies? the knots()
> function appears to return far too many knots.
> 
> I am relatively new to R, but do have good programming experience,
> though I am mostly biologist.
> 
> Thank you in advance for any inputs.
> 
> PS. An example of the histogram can be found
> here<http://photos1.blogger.com/blogger/7029/2724/1600/DU145-Bax3-Bcl-
> xL.png>
> 
>  [[alternative HTML version deleted]]
> 
> ______________________________________________
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> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
Petr Pikal
petr.pikal at precheza.cz