Hi all,
Let me preface this by saying I'm an introductory user when it comes
to R. I have a list of massive CEL files and I need to obtain the copy
numbers from them. The error message I've encountered when using the
vignette (http://www.aroma-project.org/vignettes/CRMAv1) is from the
function fit(plm, verbose=verbose), after the Summerization step. The
error, I believe, has to do with the subsequent creation of the file
"GenomeWideSNP_6,Full,monocell.CDF.tmp", with GenomeWideSNP_6,Full.cdf
being the cdf file used.
Error in list(`fit(plm, verbose = verbose)` = <environment>,
`fit.ProbeLevelModel(plm, verbose = verbose)` = <environment>, :
[2010-06-04 11:25:48] Exception: Failed to create a valid mono-cell
CDF: The cell indices are not contiguous:
at throw(Exception(...))
at throw.default("Failed to create a valid mono-cell CDF: The cell
indices are not contiguous: ", paste(udcells, collapse = ", "))
at throw("Failed to create a valid mono-cell CDF: The cell indices
are not contiguous: ", paste(udcells, collapse = ", "))
at createMonocellCdf.AffymetrixCdfFile(this, ..., verbose =
less(verbose))
at createMonocellCdf(this, ..., verbose = less(verbose))
at getMonocellCdf.AffymetrixCdfFile(cdf, ..., verbose =
less(verbose))
at getMonocellCdf(cdf, ..., verbose = less(verbose))
at getChipEffectSet.ProbeLevelModel(this, verbose = verbose)
at NextMethod("getChipEffectSet", this, ...)
at getChipEffectSet.SnpPlm(this, verbose = verbose)
at NextMethod("getChipEffectSet", this, ...)
at getChipEffectSet.CnPlm(this, verbose = verbose)
at getChipEffectSet(this, verbose = verbose)
at findUnitsTodo
Identifying non-estimated units...done
Fitting model of class RmaCnPlm...done
sessionInfo()
R version 2.11.1 (2010-05-31)
powerpc-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] aroma.affymetrix_1.6.0 aroma.apd_0.1.7
affxparser_1.20.0 R.huge_0.2.0 aroma.core_1.6.0
[6] aroma.light_1.16.0 matrixStats_0.2.1
R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.1
[11] digest_0.4.2 R.utils_1.4.0
R.oo_1.7.2 R.methodsS3_1.2.0
Can anybody enlighten me on what I'm doing wrong?
--
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/
