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"); 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/
