On Sat, Nov 5, 2011 at 7:19 PM, Henrik Bengtsson <henrik.bengts...@aroma-project.org> wrote: > Hi. > > On Fri, Nov 4, 2011 at 10:15 PM, Peter Kang <h.peter.k...@gmail.com> wrote: >> Hello, >> >> I have a question about the CRLMM algorithm implemented in Aroma. Is >> this the CRLMM v2 algorithm? > > Yes. It is implemented by porting parts of oligo as well as utilizing > existing methods in the 'oligo' package. > >> It seems the v2 algorithm is no longer >> available in the oligo package. > > I'm not aware of the status and plans of oligo/crlmm (check with their > maintainers), but at least I've just checked that in oligo v1.18.0 you > can still access the justCRLMMv2() function as: > > oligo:::justCRLMMv2 > > and it still works, cf. the following aroma.affymetrix test: > > pathname <- > "testScripts/replication/chipTypes/Mapping50K_Hind240,Xba240/test20081208,oligo,CRLMM.R"; > pathname <- system.file(pathname, package="aroma.affymetrix");
For 250K chip types, there is: pathname <- "testScripts/replication/chipTypes/Mapping250K_Nsp,Sty/test20081208,oligo,CRLMM.R"; pathname <- system.file(pathname, package="aroma.affymetrix"); /Henrik > > which is basically doing what is in the 'CRLMM genotyping (100K and > 500K)' vignette: > > http://aroma-project.org/vignettes/CRLMM100K500K > > Hope this helps > > Henrik > >> It is implemented in the crlmm >> package, but this is specific to Affy 5.0 and 6.0 arrays and Illumina, >> and the data that I have is from Affy 500k arrays. Basically I am >> looking for a CRLMM v2 algorithm implementation for Affy 500k arrays. >> >> Thanks! >> >> -- >> When reporting problems on aroma.affymetrix, make sure 1) to run the latest >> version of the package, 2) to report the output of sessionInfo() and >> traceback(), and 3) to post a complete code example. >> >> >> You received this message because you are subscribed to the Google Groups >> "aroma.affymetrix" group with website http://www.aroma-project.org/. >> To post to this group, send email to aroma-affymetrix@googlegroups.com >> To unsubscribe and other options, go to http://www.aroma-project.org/forum/ >> > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
