Dear all, I'm working on a GWAS dataset generated with the Affymetrix V2 SNP chips in the dog (http://www.broadinstitute.org/mammals/dog/caninearrayfaq.html). I'm using the aroma.package as other packages seem to not support this chip.
I've followed the manual and everything seemed to work fine, until I tried to do the "CrlmmModel" function, then I get the following error: [2014-05-22 17:23:17] Exception: Cannot fit CRLMM model: Unsupported/unsafe chip type: DogSty06m520431P at #01. CrlmmModel(ces, tags = "*,oligo") - CrlmmModel() is in environment 'aroma.affymetrix' Error: Cannot fit CRLMM model: Unsupported/unsafe chip type: DogSty06m520431P All the previous steps seemed to work fine, so I'm a bit surprised by this error. The code so far was: cdf <- AffymetrixCdfFile$byChipType("DogSty06m520431P") cdf csR <- AffymetrixCelSet$byName("OCD", cdf=cdf) csR ces <-justSNPRMA(csR, normalizeToHapmap=FALSE, returnESet=FALSE, verbose=TRUE) ces crlmm <- CrlmmModel(ces,tags="*,oligo") Can anyone help me to resolve this issue? In addition: I planned to work further with this dataset in GenABEL. Can I directly use the output from extractGenotypes as input for GenABEL? Thank you! Best regards, Bart Broeckx DVM, PhD Student Laboratory for Pharmaceutical Biotechnology Ghent University Output from sessionInfo() > sessionInfo()R version 3.0.3 (2014-03-06) Platform: x86_64-w64-mingw32/x64 (64-bit) locale:  LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252  LC_MONETARY=Dutch_Belgium.1252  LC_NUMERIC=C  LC_TIME=Dutch_Belgium.1252 attached base packages:  parallel stats graphics grDevices utils  datasets methods base other attached packages:  Biostrings_2.30.1 XVector_0.2.0  Biobase_2.22.0 oligoClasses_1.24.0  BiocGenerics_0.8.0 BiocInstaller_1.12.1  aroma.light_1.32.0 matrixStats_0.8.14  aroma.affymetrix_2.12.0 aroma.core_2.12.1  R.devices_2.9.2 R.filesets_2.4.0  R.utils_1.32.4 R.oo_1.18.0  oligo_1.26.6 IRanges_1.20.7  affxparser_1.34.2 R.methodsS3_1.6.1 loaded via a namespace (and not attached):  affyio_1.30.0 aroma.apd_0.5.0  base64enc_0.1-1 bit_1.1-12  codetools_0.2-8 DBI_0.2-7  digest_0.6.4 DNAcopy_1.36.0  ff_2.2-13 foreach_1.4.2  GenomicRanges_1.14.4 iterators_1.0.7  preprocessCore_1.24.0 PSCBS_0.41.4  R.cache_0.9.2 R.huge_0.8.0  R.rsp_0.15.0 splines_3.0.3  stats4_3.0.3 tools_3.0.3  zlibbioc_1.8.0 > traceback()No traceback available -- -- 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 email@example.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.