Dear Henrik,
I have a problem when I process my 6.0 arrays to extract CNV with CBS
(CRMA v2). Unfortunatly, seems very hard to understand my self what is
wrong from the error message. Do you have any idea?
##########################
cbs <- CbsModel(cesN)
cnrs <- getRegions(cbs, verbose=verbose)
..
..
..
20091030 10:13:32| Loading results from file...
20091030 10:13:32| Pathname: cbsData/TERATOMA,ACC,ra,-XY,BPN,-
XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/MZ15_368_testis 2A_
(GenomeWideSNP_6),chr01,f767655de5770288729dde731f43c9fc.xdr
Error in if (!grepl("RD[AX]2\n", magic)) { : argument is of length
zero
20091030 10:13:32| Loading results from file...done
20091030 10:13:32| Array #15 ('MZ15_368_testis 2A_(GenomeWideSNP_6)')
of 22 on chromosome 1...done
20091030 10:13:32| Obtaining CN model fits (or fit if missing)...done
20091030 10:13:32|Extracting regions from all fits...done
>sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods
base
other attached packages:
[1] Cairo_1.4-5 GLAD_2.0.0
DNAcopy_1.18.0
[4] xtable_1.5-5 SNPMaP_1.0.2
SNPMaP.cdm_1.0.0
[7] aroma.affymetrix_1.1.0 aroma.apd_0.1.3
R.huge_0.1.7
[10] affxparser_1.16.0 aroma.core_1.1.0
aroma.light_1.13.2
[13] matrixStats_0.1.5 R.rsp_0.3.4
R.filesets_0.5.1
[16] digest_0.3.1 R.cache_0.1.7
R.utils_1.1.6
[19] R.oo_1.4.6 R.methodsS3_1.0.3
EBImage_3.0.1
[22] abind_1.1-0
loaded via a namespace (and not attached):
[1] RColorBrewer_1.0-2 tools_2.9.0
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