[BioC] Cell cycle analysis

[Greg Finak]

Hi, Annette

On 2011-01-21, at 7:55 AM, Annette M Hynes wrote:

> Thanks, Wolfgang.  
> 
> I have looked at the different flow cytometry packages, but I haven't found anything for deconvoluting DNA histograms.  
Are you referring to 1D mixtures? The flowClust package should easily be up to the task (http://bioconductor.org/help/bioc-views/2.8/bioc/html/flowClust.html), have you tried that? Even if your data is multidimensional, flowClust is designed expressly for fitting multidimensional mixtures.

> This might be because I'm also getting blanks for many of the "reference manuals."  Have I missed something?
Forgive me for asking a naive question, but what are the "reference manuals" in this context? 

Cheers,

Greg Finak, PhD
Post-doctoral Research Associate
PS Statistics, Vaccine and Infectious Disease Division.
Fred Hutchinson Cancer Research Center
Seattle, WA
(206)667-3116
gfinak at fhcrc.org

> 
> Annette
> 
> ---------------------
> Annette M. Hynes, PhD
> Postdoctoral Research Associate
> University of Georgia
> Department of Marine Sciences
> 247 Marine Science Building
> Athens, GA  30602-3636
> tel:  706-542-2405
> 
> 
> 
> ------------------------------
> 
> Message: 13
> Date: Fri, 21 Jan 2011 01:44:53 +0100
> From: Wolfgang Huber <whuber at embl.de>
> To: bioconductor at r-project.org
> Subject: Re: [BioC] Cell cycle analysis
> Message-ID: <4D38D705.6040801 at embl.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> Annette,
> 
> besides the basic R functions for thresholding, clustering, mixture
> modelling, have you looked at the flow* packages already? -
> http://www.bioconductor.org/help/workflows/high-throughput-assays
> 
>        Best wishes
>        Wolfgang
> 
> Il Jan/20/11 5:57 PM, Annette M Hynes ha scritto:
>>  Greetings.
>> 
>> I was wondering if anyone knew of an R package for cell cycle analysis.  I would like to deconvolve DNA histograms from flow cytometry data into S, G1, and G2 phases.  Someone had asked this same question 5 years ago, and I was hoping there might have been some developments.
>> 
>> Thanks,
>> 
>> Annette
>> 
>> ---------------------
>> Annette M. Hynes, PhD
>> Postdoctoral Research Associate
>> University of Georgia
>> Department of Marine Sciences
>> 247 Marine Science Building
>> Athens, GA  30602-3636
>> tel:  706-542-2405
>> 
>>      [[alternative HTML version deleted]]
>> 
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> 
> --
> 
> 
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
> 
> 
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