Dear all,

I'm working on a GWAS dataset generated with the Affymetrix V2 SNP chips in 
the dog (
I'm using the aroma.package as other packages seem to not support this 

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$byChipType("DogSty06m520431P")
csR <- AffymetrixCelSet$byName("OCD", cdf=cdf)
ces <-justSNPRMA(csR, normalizeToHapmap=FALSE, returnESet=FALSE, verbose=TRUE)
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)

[1] LC_COLLATE=Dutch_Belgium.1252 
[2] LC_CTYPE=Dutch_Belgium.1252   
[3] LC_MONETARY=Dutch_Belgium.1252
[4] LC_NUMERIC=C                  
[5] LC_TIME=Dutch_Belgium.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils    
[6] datasets  methods   base     

other attached packages:
 [1] Biostrings_2.30.1       XVector_0.2.0          
 [3] Biobase_2.22.0          oligoClasses_1.24.0    
 [5] BiocGenerics_0.8.0      BiocInstaller_1.12.1   
 [7] aroma.light_1.32.0      matrixStats_0.8.14     
 [9] aroma.affymetrix_2.12.0 aroma.core_2.12.1      
[11] R.devices_2.9.2         R.filesets_2.4.0       
[13] R.utils_1.32.4          R.oo_1.18.0            
[15] oligo_1.26.6            IRanges_1.20.7         
[17] affxparser_1.34.2       R.methodsS3_1.6.1      

loaded via a namespace (and not attached):
 [1] affyio_1.30.0         aroma.apd_0.5.0      
 [3] base64enc_0.1-1       bit_1.1-12           
 [5] codetools_0.2-8       DBI_0.2-7            
 [7] digest_0.6.4          DNAcopy_1.36.0       
 [9] ff_2.2-13             foreach_1.4.2        
[11] GenomicRanges_1.14.4  iterators_1.0.7      
[13] preprocessCore_1.24.0 PSCBS_0.41.4         
[15] R.cache_0.9.2         R.huge_0.8.0         
[17] R.rsp_0.15.0          splines_3.0.3        
[19] stats4_3.0.3          tools_3.0.3          
[21] 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.

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