[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

Now to a trick: If you do want to distribute an AffyBatch object, have
a look at your intensities.  If your chip type is a 3x3 pixel per
probe array, and the Affymetrix image analysis (typically) took the
75% quantile (7:th ordered pixel), you will actually see only integer
probe signals.  Note, this is not a rounding error but it just happens
"by chance".  If this is the case with your data, you could create an
object holding the signals as integers and not doubles without loosing
anything.  That object would be roughly half the size.  I don't think
compression algorithms can pick this up.

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