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Affymetrix CDF Packages

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Laurent Gautier ★ 2.3k

@laurent-gautier-29

Last seen 10.2 years ago

On Thu, Oct 31, 2002 at 05:11:28PM -0500, Jeff Gentry wrote: > R packages for Affymetrix CDF data is now available on the Bioconductor > website at: http://www.bioconductor.org/data/cdfenvs/cdfenvs.html (as well > as the 'Affymetrix CDF Packages' link from the normal data page. Please > contact Rafael Irizarry (rafa@jhu.edu) with questions regarding the > packages themselves, and myself if you have questions or problems relating > to downloading of these packages. > > -Jeff > Just few words to explain what are those things (and avoid people to ask the same question). The package 'affy' went through major changes. One is that the information concerning the probe locations on a chip were extracted from the CDF files and stored in packages. This allows us to have a mechanism to link the right CDF information directly from the CEL file (and free the user to do it). This implementation also reduces a bit the memory usage (not everything contained in CDF is stored, only enough to know what is where) and improves the performances during lookups (speed). There are other advantages, which will be revealed in time... If one wants to be on the bleeding edge, it is should be already possible to do something with the devel version, but please be aware that we are still working on the toy. What are these packages could be stated somewhere on the websitei may be (like on the page where one can download the CDF packages ?). Laurent -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent

cdf probe cdf probe • 1.5k views

ADD COMMENT • link 22.1 years ago Laurent Gautier ★ 2.3k

score 0 · Answer 1 · 2002-11-01

On Thu, Oct 31, 2002 at 05:11:28PM -0500, Jeff Gentry wrote: > R packages for Affymetrix CDF data is now available on the Bioconductor > website at: http://www.bioconductor.org/data/cdfenvs/cdfenvs.html (as well > as the 'Affymetrix CDF Packages' link from the normal data page. Please > contact Rafael Irizarry (rafa@jhu.edu) with questions regarding the > packages themselves, and myself if you have questions or problems relating > to downloading of these packages. > > -Jeff > Just few words to explain what are these things. The package 'affy' is under major changes. One of them is that the probes location information contained in CDF files is extracted from there and stored in a R data structure. This was done for all the CDF we could get a hand on, and packages were created. Advantages are: - automated linking from the CEL to the CDF information package - small improvement in memory using usage (complete CDF information are no longer stored in memory when not necessary) - speed improvement when doing lookups. - other advantages that should be revealed in due time. If one wants to be on the bleeding edge, the 'devel' version of affy can probably be already tried (but be aware that we are still working on it). A short description of the nature of these packages should probably be included on the website (like on the page where one can download them)... -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent