Question: Affymetrix SDK Bioconductor package?
0
gravatar for Kasper Daniel Hansen
14.3 years ago by
Kasper Daniel Hansen630 wrote:
Is there really no-one who thinks it is a good idea to integrate the Affymetrix SDK for reading various file formats, into Bioconductor? Kasper On Sat, May 21, 2005 at 10:58:19AM -0700, James Bullard wrote: > > Hi all, we have been working for the last month or so on integrating the > Affymetrix parsing SDK 2.0 into an R package. We began because we had a > CDF file which would not parse with the existing libraries in > Bioconductor (the problem turned out to be in the CDF file itself). In > any case, we have spent a good amount of time on providing an interface > to this package in R, specifically duplicating the interfaces which are > currently available in Bioconductor to the CDF, CEL, CHP, BPMAP, and BAR > files (where relevant). One of the nice things about the library is that > binary formats are also accepted so the same interface can parse both > text and binary transparently. Also, it should be much easier to absorb > new library changes when Affymetrix releases new SDKs and file formats. > > The library still needs some work, but before I spend a *lot* more time > on it I wanted to know 1.) if people thought this would be good thing to > have and 2.) if someone was already working on integrating these libraries. > > We are hopeful that people will think this is a good idea - we cannot > see any reason why this would not be a good addition to Bioconductor, > and would very much like to finish the work with the blessing of the > BioC community. > > Thanks, jim > > -- > James Bullard > bullard@berkeley.edu > 760.267.0986 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen
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ADD COMMENTlink modified 14.3 years ago by Seth Falcon7.4k • written 14.3 years ago by Kasper Daniel Hansen630
Answer: Affymetrix SDK Bioconductor package?
0
gravatar for A.J. Rossini
14.3 years ago by
A.J. Rossini210
A.J. Rossini210 wrote:
Sure it's a good idea (under the constraints/caveats of licensing, support, etc). Why not? On 6/1/05, Kasper Daniel Hansen <k.hansen@biostat.ku.dk> wrote: > Is there really no-one who thinks it is a good idea to integrate the > Affymetrix SDK for reading various file formats, into Bioconductor? > > Kasper > > On Sat, May 21, 2005 at 10:58:19AM -0700, James Bullard wrote: > > > > Hi all, we have been working for the last month or so on integrating the > > Affymetrix parsing SDK 2.0 into an R package. We began because we had a > > CDF file which would not parse with the existing libraries in > > Bioconductor (the problem turned out to be in the CDF file itself). In > > any case, we have spent a good amount of time on providing an interface > > to this package in R, specifically duplicating the interfaces which are > > currently available in Bioconductor to the CDF, CEL, CHP, BPMAP, and BAR > > files (where relevant). One of the nice things about the library is that > > binary formats are also accepted so the same interface can parse both > > text and binary transparently. Also, it should be much easier to absorb > > new library changes when Affymetrix releases new SDKs and file formats. > > > > The library still needs some work, but before I spend a *lot* more time > > on it I wanted to know 1.) if people thought this would be good thing to > > have and 2.) if someone was already working on integrating these libraries. > > > > We are hopeful that people will think this is a good idea - we cannot > > see any reason why this would not be a good addition to Bioconductor, > > and would very much like to finish the work with the blessing of the > > BioC community. > > > > Thanks, jim > > > > -- > > James Bullard > > bullard@berkeley.edu > > 760.267.0986 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- > Kasper Daniel Hansen, Research Assistant > Department of Biostatistics, University of Copenhagen > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- best, -tony "Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes" (AJR, 4Jan05). A.J. Rossini blindglobe@gmail.com
ADD COMMENTlink written 14.3 years ago by A.J. Rossini210
Answer: Affymetrix SDK Bioconductor package?
0
gravatar for Seth Falcon
14.3 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Hi James, On 21 May 2005, bullard@berkeley.edu wrote: > We are hopeful that people will think this is a good idea - we > cannot see any reason why this would not be a good addition to > Bioconductor, and would very much like to finish the work with the > blessing of the BioC community. Extending Bioconductor's ability to parse binary Affy data sounds like a good thing, as long as there are no license issues with respect to the Affymetrix SDK (as Tony mentioned). If I understand what you've described, the logical place for this functionality would be in the affy package itself (not another package that duplicates existing functionality). So a good starting point would be to contact Raphael, the affy maintainer (see DESCRIPTION file of affy). In general, this sort of extending/adding-on/improving of existing packages is very much appreciated and possibly even blessed :-) Best Wishes, + seth
ADD COMMENTlink written 14.3 years ago by Seth Falcon7.4k
Just to be really clear, what we are talking about is an interface to http://www.affymetrix.com/support/developer/filesdk/index.affx?terms=n o which is a C++ library which can parse CEL, CHP, CDF, BPMAP, BAR files. Several of these file formats are already readable by BioC, but I still think it is nice to have an interface to an official parsing library. The license used is LGPL-2, so there should be no problem there - right? Kasper On Thu, Jun 02, 2005 at 06:47:56AM -0700, Seth Falcon wrote: > Hi James, > > On 21 May 2005, bullard@berkeley.edu wrote: > > We are hopeful that people will think this is a good idea - we > > cannot see any reason why this would not be a good addition to > > Bioconductor, and would very much like to finish the work with the > > blessing of the BioC community. > > Extending Bioconductor's ability to parse binary Affy data sounds like > a good thing, as long as there are no license issues with respect to > the Affymetrix SDK (as Tony mentioned). > > If I understand what you've described, the logical place for this > functionality would be in the affy package itself (not another package > that duplicates existing functionality). So a good starting point > would be to contact Raphael, the affy maintainer (see DESCRIPTION file > of affy). > > In general, this sort of extending/adding-on/improving of existing > packages is very much appreciated and possibly even blessed :-) > > Best Wishes, > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen
ADD REPLYlink written 14.3 years ago by Kasper Daniel Hansen630
Correct. On 6/2/05, Kasper Daniel Hansen <k.hansen@biostat.ku.dk> wrote: > Just to be really clear, what we are talking about is an interface to > http://www.affymetrix.com/support/developer/filesdk/index.affx?terms =no > which is a C++ library which can parse CEL, CHP, CDF, BPMAP, BAR files. > Several of these file formats are already readable by BioC, but I still > think it is nice to have an interface to an official parsing library. > > The license used is LGPL-2, so there should be no problem there - right? > > Kasper > > On Thu, Jun 02, 2005 at 06:47:56AM -0700, Seth Falcon wrote: > > Hi James, > > > > On 21 May 2005, bullard@berkeley.edu wrote: > > > We are hopeful that people will think this is a good idea - we > > > cannot see any reason why this would not be a good addition to > > > Bioconductor, and would very much like to finish the work with the > > > blessing of the BioC community. > > > > Extending Bioconductor's ability to parse binary Affy data sounds like > > a good thing, as long as there are no license issues with respect to > > the Affymetrix SDK (as Tony mentioned). > > > > If I understand what you've described, the logical place for this > > functionality would be in the affy package itself (not another package > > that duplicates existing functionality). So a good starting point > > would be to contact Raphael, the affy maintainer (see DESCRIPTION file > > of affy). > > > > In general, this sort of extending/adding-on/improving of existing > > packages is very much appreciated and possibly even blessed :-) > > > > Best Wishes, > > > > + seth > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- > Kasper Daniel Hansen, Research Assistant > Department of Biostatistics, University of Copenhagen > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- best, -tony "Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes" (AJR, 4Jan05). A.J. Rossini blindglobe@gmail.com
ADD REPLYlink written 14.3 years ago by A.J. Rossini210
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