I'm trying to run normalisation of CytoScan HD arrays, and have problems
getting the CRMAv2 pre-processing to run as in the
Vignett<http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis>.
The instruction
dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
fails with the error message
Failed with error: ‘package ‘sfit’ was built before R 3.0.0: please
re-install it’
which is the same I get from calling library("sfit"). However, I cannot
find a newer version/build of sfit to install.
Installation attempts include
source("http://bioconductor.org/biocLite.R";)
biocLite("sfit")
and
install.packages("sfit", repos="http://R-Forge.R-project.org";)
and
source("http://www.braju.com/R/hbLite.R";)
hbLite("sfit")
and more, but with the same error when trying to import it.
I upgraded to R 3.0.1 and reinstalled Bioconductor after previous attempts
at running the script complained that some parts were outdated.
Here's the session info and traceback:
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] R.cache_0.7.1 aroma.affymetrix_2.9.5 affxparser_1.32.3
[4] aroma.apd_0.2.3 R.huge_0.4.1 aroma.light_1.30.2
[7] aroma.core_2.9.6 matrixStats_0.8.5 R.rsp_0.9.10
[10] R.devices_2.2.2 R.filesets_2.0.1 R.utils_1.25.2
[13] R.oo_1.13.9 R.methodsS3_1.4.4
loaded via a namespace (and not attached):
[1] digest_0.6.3 PSCBS_0.35.0 tools_3.0.1
> traceback()
15: stop(cond)
14: throw.Exception(Exception(...))
13: throw(Exception(...))
12: throw.default("Package not loaded: sfit")
11: throw("Package not loaded: sfit")
10: fitGenotypeConeBySfit.matrix(y, ...)
9: fitGenotypeConeBySfit(y, ...)
8: fitGenotypeCone.matrix(y, flavor = flavor, alpha = alpha, q = q,
Q = Q, verbose = verboseL)
7: fitGenotypeCone(y, flavor = flavor, alpha = alpha, q = q, Q = Q,
verbose = verboseL)
6: process.AllelicCrosstalkCalibration(acc, verbose = verbose)
5: process(acc, verbose = verbose)
4: doCRMAv2.AffymetrixCelSet(csR, ..., verbose = verbose)
3: doCRMAv2(csR, ..., verbose = verbose)
2: doCRMAv2.default(dataSet, cdf = cdf, combineAlleles = FALSE,
verbose = verbose)
1: doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = verbose)
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