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:
[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.
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/
---
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.
