Affymetrix SDK Bioconductor package?
2
0
Entering edit mode
@kasper-daniel-hansen-459
Last seen 8.0 years ago
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
cdf cdf • 745 views
ADD COMMENT
0
Entering edit mode
A.J. Rossini ▴ 210
@aj-rossini-973
Last seen 8.0 years ago
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 COMMENT
0
Entering edit mode
Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 8.0 years ago
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 COMMENT
0
Entering edit mode
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 REPLY
0
Entering edit mode
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 REPLY

Login before adding your answer.

Traffic: 338 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6