Dear Marc and Francois, I have just gone through the process of retrieving the new annotation files from Agilent's earray web site and I can confirm that is *is* a pain. :-) Of course I'll be more than happy to make a contribution in exchange for the first-class software and support we have enjoyed for many years and I'm probably better in dealing with annotation than in devising innovative statistical methods anyway... so I'll have a look at the packages/vignettes Marc has mentioned and will for sure come back with further questions... Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland From: Marc Carlson <mcarlson at="" fhcrc.org=""> To: Francois Pepin <francois at="" sus.mcgill.ca=""> Cc: bioconductor at stat.math.ethz.ch Date: 26.08.2010 18:45 Subject: Re: [BioC] annotation for new agilent arrays Sent by: bioconductor-bounces at stat.math.ethz.ch Hi Francois, The troublesome part is not really adding things into the pipeline for building, it's the fact that Agilent does not make it easy for me to automate updates for their probe mapping files. When you combine that with the fact that we are already building, checking and hosting about 120 annotation packages twice a year here you can hopefully see that this process is not truly devoid of cost. The result is that it's never quite as simple as just pushing a button to get all these things built, checked, and tested etc. Most of it is automatic, but some of it (like getting new mapping files from Agilent (or other more boutique platforms) cannot be easily automated. Having package contributors is also not free of cost. I do still have to bother them twice a year and make sure that things get built correctly etc. But it is still a big win for the project to have people contribute because it means that we cover more ground from more different kinds of platforms than I might think to include on my own and also because it means that we can support more packages overall right out of the box. So I guess what I am saying is that package contributors are extremely helpful to the project and should always be encouraged. ;) If you have some ideas for how I can make this even more automatic and want to discuss it further I would be happy to, but at this point we should probably consider taking it offline as I think the discussion is maybe no longer relevant to the entire thread. ;) Marc On 08/25/2010 04:52 PM, Francois Pepin wrote: > Hi Marc, > > How much work would it be to just include those in your pipeline? > > The process should be exactly the same as for the current agilent arrays (like hgug4112a, mgug4122a). Considering the current use of Agilent arrays, I think the new versions are going to be relatively widely used for a bit longer. > > Francois > > On Aug 25, 2010, at 1:58 PM, Marc Carlson wrote: > > >> Hi Axel, >> >> We always welcome new annotation packages. But be warned that you would >> be expected to maintain them and provide a updated version of them for >> each release of Bioconductor. That works out to me sending you an email >> (requesting an update) twice a year. The SQLForge package should allow >> you to make a new annotation package. You can see the vignette that is >> bundled in the AnnotationDbi package for details. >> >> >> Marc >> >> >> >> On 08/25/2010 08:37 AM, axel.klenk at actelion.com wrote: >> >>> Dear Bioc list and esp. Marc, >>> >>> are there any plans to include annotation for the new Agilent 4x44K v2/v3 >>> and 8x60K arrays in one of the next releases of Bioconductor? As far as I >>> understand the non-control oligo set is the same for 4x44K v2 and 8x60K. >>> We'd be interested in human (G4845A), mouse (G4868A) and rat (G4847B) >>> in particular. >>> >>> If not, and if I should succeed in creating such packages myself :-), >>> would >>> you want to obtain and distribute the results of these efforts? >>> >>> Cheers, >>> >>> - axel >>> >>> >>> Axel Klenk >>> Research Informatician >>> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / >>> Switzerland >>> >>> >>> >>> The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. >>> It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. 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For further information about Actelion please see our website at http://www.actelion.com >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com