Re: offer from I Neuhaus to create a BMS response; keep in core, please

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Rafael A. Irizarry ★ 2.3k

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On Tue, 1 Jul 2003, Robert Gentleman wrote: <snip> > Vis a vis the phone call, it was about 1 hour long, it was slightly > focussed on marketing hype on their side and some substantial, > although peculiar concerns came out. One of the major concerns that > they have is that if they make their formats public then anyone can > create a "CEL" file of the right format and make it look very much > like one that they generated. They believe that this would lead to > substantial confusion. To some extent I agree with them and I think > that I would be inclined to discourage any such activity, and I hope > BioC as a group would too (since it really spreads confusion, when > opening a CEL file we want to be pretty sure where it came from and > what is in it). > i just rememebered, in the affy package there is a function called write.celfile should we remove this? <snip>

affy affy • 930 views

ADD COMMENT • link updated 20.8 years ago by Todd Richmond ▴ 140 • written 20.8 years ago by Rafael A. Irizarry ★ 2.3k

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Todd Richmond ▴ 140

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Last seen 9.6 years ago

> -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Rafael A. > Irizarry > Sent: Tuesday, July 01, 2003 8:14 AM > To: bioconductor@stat.math.ethz.ch > > On Tue, 1 Jul 2003, Robert Gentleman wrote: > > <snip> > > Vis a vis the phone call, it was about 1 hour long, it was slightly > > focussed on marketing hype on their side and some substantial, > > although peculiar concerns came out. One of the major concerns that > > they have is that if they make their formats public then anyone can > > create a "CEL" file of the right format and make it look very much > > like one that they generated. They believe that this would lead to > > substantial confusion. That doesn't make a lot of sense. If they are concerned about the authenticity of "CEL" files can't they just use a digital signature, or some sort of checksum scheme for verification? I can't imagine that a binary format is going to make life easier for anyone. If they are concerned about size, there are standard compression libraries that you can use to compress/uncompress your data files on-the-fly as you save/load. Todd -- Todd Richmond Manager of Research Informatics NimbleGen Systems, Inc One Science Court Madison, WI 53711 Ph: 1-608-218-7651

ADD COMMENT • link 20.8 years ago Todd Richmond ▴ 140

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Todd Richmond wrote: >>-----Original Message----- >>From: bioconductor-bounces@stat.math.ethz.ch >>[mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Rafael A. >>Irizarry >>Sent: Tuesday, July 01, 2003 8:14 AM >>To: bioconductor@stat.math.ethz.ch >> >>On Tue, 1 Jul 2003, Robert Gentleman wrote: >> >><snip> >> >> >>>Vis a vis the phone call, it was about 1 hour long, it was slightly >>>focussed on marketing hype on their side and some substantial, >>>although peculiar concerns came out. One of the major concerns that >>>they have is that if they make their formats public then anyone can >>>create a "CEL" file of the right format and make it look very much >>>like one that they generated. They believe that this would lead to >>>substantial confusion. >>> >>> > >That doesn't make a lot of sense. If they are concerned about the >authenticity of "CEL" files can't they just use a digital signature, or some >sort of checksum scheme for verification? > Am I missing something? Do they want to patent their own CEL format? (sorry just being facetious) >I can't imagine that a binary >format is going to make life easier for anyone. If they are concerned about >size, there are standard compression libraries that you can use to >compress/uncompress your data files on-the-fly as you save/load. > I disagree. A binary file could facilitate getting chunks of data using random access without having to go through the whole file. For example, you can imagine at some point creating you own 'probe sets' with features that are different than those mapped by Affy. However the structure of the file MUST be publicly available. I > >Todd > >-- >Todd Richmond >Manager of Research Informatics >NimbleGen Systems, Inc >One Science Court >Madison, WI 53711 >Ph: 1-608-218-7651 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >

ADD REPLY • link 20.8 years ago Isaac Neuhaus ▴ 360

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> >I can't imagine that a binary > >format is going to make life easier for anyone. If they are > concerned about > >size, there are standard compression libraries that you can use to > >compress/uncompress your data files on-the-fly as you save/load. > > > I disagree. A binary file could facilitate getting chunks of data using > random access without having to go through the whole file. For example, > you can imagine at some point creating you own 'probe sets' with > features that are different than those mapped by Affy. However the > structure of the file MUST be publicly available. While that's certainly true, you can achieve the same goal with a plain text file using memory-mapped files and/or indexing schemes. Of course, using compression is probably out then. But disk space and memory are cheap - I'd rather have readily accessible (and human-readable) text formats than proprietary binary formats (even if their structure/format is publicly available and well-documented). Of course, I'm speaking from a purely selfish point of view. We have our own equivalents of CEL/CDF files, though ours are all just tab-delimited text files. If the affy package migrates to binary files and proprietary APIs to keep in step with Affymetrix, it will become more and more difficult for us to utilize the Bioconductor tools. There's already a lot of affy specific assumptions in the oligo array tools that cause problems for us - rightly so since it's the "affy" package. I'd rather see a trend toward more generalized tools than tools that are highly specific to a single platform. But that's because I'm lazy - I don't want to have to re-code all of the "affy" package to make an equivalent "ngs" package. Regards, Todd -- Todd Richmond Manager of Research Informatics NimbleGen Systems, Inc One Science Court Madison, WI 53711 Ph: 1-608-218-7651

ADD REPLY • link 20.8 years ago Todd Richmond ▴ 140

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