[Bioc-devel] Package size limitation
Thanks everyone, I found what I needed! Cheers, ------------------------------ Tobias Guennel Research Assistant Department of Biostatistics Virginia Commonwealth University Theater Row 3035F 804-828-2527 -----Original Message----- From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org] Sent: Friday, August 01, 2008 12:27 PM To: Kasper Daniel Hansen Cc: Tobias Guennel; bioc-devel at stat.math.ethz.ch Subject: Re: [Bioc-devel] Package size limitation Tobias, To elaborate on Kasper's well-stated points, the Bioconductor project has separate repositories for software, experiment data, and annotation metadata. BioC software: http://bioconductor.org/packages/release/bioc/ BioC experiment data: http://bioconductor.org/packages/release/data/experiment/ BioC annotation metadata: http://bioconductor.org/packages/release/data/annotation/ The main criterion for an experiment data package is that it should be novel in some way to make it useful for other software developers to utilize it when illustrating concepts in their software package. More often than not, including a subset of your data in your software package will suffice. One common misconception by new package developers is that examples in the man pages and the vignettes need to be 100% "real". The main goal of vignettes and man pages is to illustrate concepts rather than reveal scientific findings. You are encouraged to provide references to scientific papers that demonstrate the latter within your software's documentation, but typically end-users want your package to have a small storage footprint on their machine and have the examples run in a short time frame. If you are not sure how to handle your particular situation, when the Bioconductor team previews and reviews your package, we will help you through any tricky decisions. Good luck with your package submission and thanks for your interest in the Bioconductor project! Patrick
Kasper Daniel Hansen wrote:
I believe the right way to do this is the following 1) Make an AffyBatch containing only a few probesets to use for your examples. Include this in the package 2) Submit a package containing your experiment 3) Use the package above in a vignette. But I am sure someone else will chime in. Kasper On Jul 31, 2008, at 8:22 PM, Tobias Guennel wrote:
Dear all, I'm writing my first R package that I want to submit to Bioconductor implementing an algorithm for detecting differentially expressed genes that is not available in R yet. The example data set is an AffyBatch object that contains 6 read in *.CEL files, which were used in the paper introducing the algorithm and are most suitable to show the application of the package. Unfortunately, including the data example increases the size of the compressed package to 6MB. Is there a way to drastically reduce the size of an Affybatch object or are there other options that can reduce the file size? Thanks for your help, ------------------------------ Tobias Guennel Research Assistant Department of Biostatistics Virginia Commonwealth University Theater Row 3035F 804-828-2527
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