Dear Group, Affymetrix recently launched arrays for exon analysis, containing approx. 1.4 million probe sets. Athough some methods for detection of alternative splicing events (MIDAS, PAC) have been described in Affymetrix White Papers, these algorithms do not seem to be implemented anywhere. Does anybody have these or other tools for the analysis of Affyon arrays (detection of alternative splicing events) available, maybe as R code or so? Any help would be greatly appreciated. Sincerely Reinhard -- Dr. Reinhard Hoffmann Email: r_hoffmann at m3401.mpk.med.uni-muenchen.de -----BEGIN PGP PUBLIC KEY BLOCK----- Version: PGP 8.0.1 - nicht f?r kommerzielle Nutzung lizenziert: www.pgp.com mQGiBEBiqn0RBADD7cwc5NHH98xZUn0hG53uL1nw2aVRXwurSWjqK5ytCUh2ZqB4 f/td9yCpQP3KYTzt4oW0wLK80OOvQ6twiozh49lcxWBGw4aY29RZADrV341MbJZm mcwp03VKaV++x+lEPepjUrIZQpYh5YMdnlFBMBF7J5jyS7LU22qbV+KwVwCg/8PI HO7/xBgu5JBYLP10O1sBSPkEAIZptRAYY4GO8hSX60Go8bSjLm/M/2lwYNqueSL/ AwYFR6OqCnBCAtjrv8YLB0puAso2GsSXJd6kjHDWBIzFaBwaPxNcIkYvbVycaByk zSvucM9EqR6fUzm4TDelCH+ISAeRa1gUOf9H1q7f0iPFKeaETSaPk2LX6QhJlnn/ /jfyBACOsbsZuM0uUGAbATa9ioS3ssQ8LVM0aiZaNUsEzsjb/8N7FPmKnqG5o1Aq PCIbk2Vk7f1IOZdJmBPXH70hLMJHHOyGmTBYFpscAUHMa7wlqJjVoVVu9On+Wa1u YnKWRrfdgSCIWc/x9JE6nKtAhykIeWTcuaOmQ+Z8qvz7/iGso7RARHIuIFJlaW5o YXJkIEhvZmZtYW5uIDxyX2hvZmZtYW5uQG0zNDAxLm1way5tZWQudW5pLW11ZW5j aGVuLmRlPokAWAQQEQIAGAUCQGKqfQgLCQgHAwIBCgIZAQUbAwAAAAAKCRDRdQPa E3rr/yoYAKDZn0r8AbkVwZCowvO4hyTbBSeuBQCfYdWSBK+UDk5oDBl/dHj9vz0L 6JC5Ag0EQGKqfRAIAPZCV7cIfwgXcqK61qlC8wXo+VMROU+28W65Szgg2gGnVqMU 6Y9AVfPQB8bLQ6mUrfdMZIZJ+AyDvWXpF9Sh01D49Vlf3HZSTz09jdvOmeFXklnN /biudE/F/Ha8g8VHMGHOfMlm/xX5u/2RXscBqtNbno2gpXI61Brwv0YAWCvl9Ij9 WE5J280gtJ3kkQc2azNsOA1FHQ98iLMcfFstjvbzySPAQ/ClWxiNjrtVjLhdONM0 /XwXV0OjHRhs3jMhLLUq/zzhsSlAGBGNfISnCnLWhsQDGcgHKXrKlQzZlp+r0ApQ mwJG0wg9ZqRdQZ+cfL2JSyIZJrqrol7DVekyCzsAAgIIAMQrT0Bic9AFu456+JXR qFT58G/mB/JSdvlbueq+8Sr0W4x7KdJ7uxKV+Iuk557pbAbP6WnBHeG3t0p0jCTr kAt4rLVAHS3Yz8j4M1q3K45TWFB0AjgKGVM8JvWlgYHWYRzSAMVMtjH+Jhr3SoBh 4ZnpmlWJ0rhKF7V4ioC4fOtz+BM3CnPyRi2effevIGbIM4zC4C0jxY6Hy9JecvJh 2j35D5gHiJWvHUXYCtdSBNLYDEmSmK5WuoEY7FjskyTd70wbM8lv+zwyKpq6kqnc XverpxyU49chB3Do9seEMWHZZTPfzKfJRHPIOCsjU3GTiQkbl1zDz1FgOZ4Xx539 dg6JAEwEGBECAAwFAkBiqn0FGwwAAAAACgkQ0XUD2hN66/8VDwCgq/2PAsRp0rAX iXS1T2bL7Fow9zUAnAtzantYb0tV+Iw603AsKQjyDPBW =LGSI -----END PGP PUBLIC KEY BLOCK-----

Hi Reinhard and BioC We've been using affy tiling arrays in Arabidopsis for alternative splicing. The method is straight forward once exons or transcription subunits (parts of known alternative exons) are defined. We first look for differential gene expression according to the treatment, time or your contrast. Use your favorite package, limma, siggenes etc. Take the residuals from the model. Now all genes have been corrected for alternative expression, look again at the contrast for alternative transcription subunits, using your favorite method. In our case its about 25k genes and 120k subunits tested for alternative splicing. The key is one is limited to get an idea for alternative splicing within a gene in a single condition given the large variance in probe effects, what does that mean biologically anyhow. What one has power for is alternative splicing across conditions. Finally there is a semantic argument to be made, what does alternative gene expression mean if there is alternative splicing? One could put both gene expression and splicing in a single model, here though one exon would have to be a reference, others are tested for an exon:treatment interaction effect. If that reference exon was alternatively spliced, it would be taken as the gene expression difference and all the other exons alternatively spliced. Any how I just like to fit the models separately, its easier to think about and explain. Gene expression is difference in overall means using all probes(exons). Alternative splicing is a difference across probes in a subunit. Hope it helps.. We can provide code but it's in a format for tiling arrays not yet an affybatch Justin ----- Justin Borevitz Ecology and Evolution (CLSC 915E) University of Chicago 1101 E. 57th St. Chicago, IL 60637 USA (773) 702-5948 office (773) 834-4055 lab borevitz at uchicago.edu http://naturalvariation.org _____________________________ Dear Group, Affymetrix recently launched arrays for exon analysis, containing approx. 1.4 million probe sets. Athough some methods for detection of alternative splicing events (MIDAS, PAC) have been described in Affymetrix White Papers, these algorithms do not seem to be implemented anywhere. Does anybody have these or other tools for the analysis of Affyon arrays (detection of alternative splicing events) available, maybe as R code or so? Any help would be greatly appreciated. Sincerely Reinhard -- Dr. Reinhard Hoffmann

Yes this one limitation, the annotation for new arrays. So far we have done our own and can share with other Arabidopsis people if there is interest. We have developed methods for SFP (polymorphism detection) http://naturalvariation.org/sfp http://naturalvariation.org/methods and are toying with novel gene prediction. Novel gene prediction is a crucial area. I'd like to hear others approaches toward it. Hidden markov models are something we have been thinking of. Antisense expression is another related and open area when strand specific expression is available. Chip/chip and methylome analysis are others. I expect methods to come out in the next year as the arrays become more widely available. http://naturalsystems.org/BorevitzEckerAnnualReview.pdf ----- Justin Borevitz > -----Original Message----- > From: Thomas Girke [mailto:thomas.girke at ucr.edu] > Sent: Thursday, October 20, 2005 12:51 PM > To: Justin Borevitz > Subject: Re: [BioC] Affy Exon Array Analysis > > Dear Justin, > > Are there any BioC annotation packages (metadata) available for the > Affy tiling arrays? If not could you explain how you performed the > primary data analysis in R starting from cel files? > > A more general question to the mailing list: what type of BioC anlaysis > tools are currently under development to deal with the many additional > data outputs from tiling arrays, e.g. mutant analysis, SNP and novel > gene detection, etc. > > Thanks for posting this info. > > Thomas > > > > On Thu 10/20/05 08:24, Justin Borevitz wrote: > > Hi Reinhard and BioC > > We've been using affy tiling arrays in Arabidopsis for alternative > splicing. > > The method is straight forward once exons or transcription subunits > (parts > > of known alternative exons) are defined. We first look for differential > > gene expression according to the treatment, time or your contrast. Use > your > > favorite package, limma, siggenes etc. Take the residuals from the > model. > > Now all genes have been corrected for alternative expression, look again > at > > the contrast for alternative transcription subunits, using your favorite > > method. In our case its about 25k genes and 120k subunits tested for > > alternative splicing. The key is one is limited to get an idea for > > alternative splicing within a gene in a single condition given the large > > variance in probe effects, what does that mean biologically anyhow. > What > > one has power for is alternative splicing across conditions. > > > > Finally there is a semantic argument to be made, what does alternative > gene > > expression mean if there is alternative splicing? One could put both > gene > > expression and splicing in a single model, here though one exon would > have > > to be a reference, others are tested for an exon:treatment interaction > > effect. If that reference exon was alternatively spliced, it would be > taken > > as the gene expression difference and all the other exons alternatively > > spliced. Any how I just like to fit the models separately, its easier > to > > think about and explain. Gene expression is difference in overall means > > using all probes(exons). Alternative splicing is a difference across > probes > > in a subunit. > > > > Hope it helps.. We can provide code but it's in a format for tiling > arrays > > not yet an affybatch > > Justin > > ----- > > Justin Borevitz > > Ecology and Evolution (CLSC 915E) > > University of Chicago > > 1101 E. 57th St. > > Chicago, IL 60637 USA > > (773) 702-5948 office > > (773) 834-4055 lab > > borevitz at uchicago.edu > > http://naturalvariation.org > > > > _____________________________ > > Dear Group, > > Affymetrix recently launched arrays for exon analysis, containing > > approx. 1.4 million probe sets. Athough some methods for detection of > > alternative splicing events (MIDAS, PAC) have been described in > > Affymetrix White Papers, these algorithms do not seem to be > > implemented anywhere. > > Does anybody have these or other tools for the analysis of Affyon > > arrays (detection of alternative splicing events) available, maybe as > > R code or so? Any help would be greatly appreciated. > > Sincerely Reinhard > > > > -- > > Dr. Reinhard Hoffmann > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > -- > Thomas Girke > University of California > Riverside, CA 92521