> 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 setupâ¦): 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 â, >> 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 â¦). >> >> 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.ramba...@ieo.eu >> [e] davide.ramba...@gmail.com >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]]
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