[Bioc-devel] I would like to publish a bioconductor package.

[Stephanie M. Gogarten]

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 at parentPeakPosition,  parent.fitting.cfse at 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 at ieo.eu
> [e] davide.rambaldi at gmail.com
>
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