
> You can solve the package size issue by putting your example data in a separate "experiment data" package (http://www.bioconductor.org/packages/release/data/experiment/).
> 
> Stephanie


I fixed the package size issue with a secondary experiment data package (flowFitExampleData)

It is not clear to me how to fix the dependencies between the 2 packages:

My setup (I am trying to duplicate the affy/affydata setup…):

flowFit/DESCRIPTION

Suggests: flowFitExampleData


flowFitExampleData/DESCRIPTION

Depends: flowFit


And a lot of (may be are not necessary?)

if (require(flowFItExampleData)) 

in the examples

 It is correct?

Davide

P.S:

 tested the package on OSX and Linux with R 3.0 unstable for BUILD and CHECK and it's OK… (me vs inconsolata.sty: 1 -0)

 for windows, well I will try to do it … may be I will ask more help ...



On Feb 27, 2013, at 5:25 PM, Stephanie M. Gogarten wrote:

> You can solve the package size issue by putting your example data in a separate "experiment data" package (http://www.bioconductor.org/packages/release/data/experiment/).
> 
> Stephanie
> 
> On 2/27/13 3:03 AM, Davide Rambaldi wrote:
>> Hi all,
>> 
>> I am working on a library called flowFit, the purpose of this library is to analyze the FACS data coming from proliferation tracking dyes study.
>> 
>> The library depends on the flowCore and flowViz bioconductor libraries and use minpack.lm (levenberg-marquadt algorithm) to fit a set of peaks over the FACS data.
>> 
>> A typical experimental pipeline:
>> 
>> 1) Acquire with FACS a sample of unlabelled cells
>> 2) Acquire with FACS a sample of labeled and unstimulated cells (the Parent Population)
>> 3) Acquire with FACS a sample of labeled and stimulated cells (the Proliferative Population)
>> 
>> In R we can use the flowCore functions to transform the raw data and to gate the population of interest. Once we have gated the correct population, with 2 commands of flowFit you can perform the fitting:
>> 
>>> library(flowFit)
>>> parent <- parentFitting(QuahAndParish[[1]], "<FITC-A>")
>>> fitting <- proliferationFitting(QuahAndParish[[2]],  "<FITC-A>", parent.fitting.cfse@parentPeakPosition,  parent.fitting.cfse@parentPeakSize)
>> 
>> The function can generate also some graphical output with:
>> 
>>> plot(fitting.cfse)
>> 
>> To demonstrate the correctness of the fitting I have made some in silico simulations and a retrospective analysis of the data from the paper:
>> 
>> "New and improved methods for measuring lymphocyte proliferation in vitro and in vivo using CFSE-like fluorescent dyes", Benjamin J.C. Quah ⁎, Christopher R. Parish, Journal of Immunological Methods (2012)
>> 
>> In this paper, the same population of lymphocytes (proliferation with the same growth conditions) was stained with 3 different proliferation tracking dyes: if the fitting algorithm is working as expected, we expect to estimate the same % of cells for generation in the 3 sample.
>> 
>> Comparing the 3 samples we didn't see any significant difference in the estimation of the % of cell for generations, suggesting us that the algorithm is correctly estimating the % of cells / generation.
>> 
>> I have posted a graphical output example with the Quah and Parish data (pdf) here:
>> 
>> http://dl.dropbox.com/u/40644496/QuahAndPArishOut.pdf
>> 
>> The dataset will be included in the library (in the data subdir).
>> 
>> Actually I am writing the vignette (I am following the guidelines in http://www.bioconductor.org/developers/package-guidelines/) and fixing some graphical bugs (like the legend oversized …).
>> 
>> The package Pass R CMD build and R CMD CHECK (time: 86 seconds) with no errors on OSX and Linux (I have to find a windows machine somewhere ...), I still have to test with the R-devel version of R.
>> 
>> The library is bigger than expected (4.2 Mb) because the example datasets (FCS files converted in .Rdata) are big (3.7M) and I don't know how to solve this issue...
>> 
>> My question is, How I proceed from here?
>> 
>> I would like to publish the library/methods in a paper (Bioinformatics Journal may be?) and submit the library to Bioconductor, which is the correct way to proceed?
>> 
>> Thanks
>> 
>> P.S: If I miss (again!) some FAQ please apologize me
>> 
>> -----------------------------------------------------
>> Davide Rambaldi, PhD.
>> -----------------------------------------------------
>> IEO ~ MolMed
>> [e] davide.rambaldi@ieo.eu
>> [e] davide.rambaldi@gmail.com
>> 
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> _______________________________________________
> Bioc-devel@r-project.org mailing list
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