Dear all,
I have finished CBS step. Now I got some error message when I try to
generate figures. In the output folder, neither figures nor
regions.xls files were generated. Would you please give me some
suggestions how to fix the problem?
Thanks,
Qian
>#CBS Model
>sm_test<- CbsModel(cesNList[[2]],ceR)
>fit(sm_test,chromosomes=1:22, verbose=-10);
>ce_test <- ChromosomeExplorer(sm_test)
># Arrays to be modelled
>setArrays(ce_test,"array 1")
># Use a different data set name for the output
>setAlias(ce_test, "20 test samples")
>print(ce_test)
>process(ce_test,chromosomes=c(19,22), verbose=verbose)
Generating ChromosomeExplorer report...
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file '/
***********************************************************************
* The file was automatically generated by aroma.affymetrix.
* Do not edit this file!
***********************************************************************/
explorer.onLoad = function() {
/* Detected chip types */
this.setChipTypes(new Array(': No such file or directory
Generating ChromosomeExplorer report...done
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252
LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets utils methods
base
other attached packages:
[1] DNAcopy_1.28.0 gcrma_2.26.0
Biobase_2.14.0
[4] preprocessCore_1.16.0 aroma.affymetrix_2.3.0
affxparser_1.26.1
[7] aroma.apd_0.2.0 R.huge_0.3.0
aroma.core_2.3.1
[10] aroma.light_1.22.0 matrixStats_0.4.0
R.rsp_0.6.7
[13] R.filesets_1.1.3 digest_0.5.1
R.cache_0.5.2
[16] BiocInstaller_1.2.1 R.utils_1.9.3
R.oo_1.8.3
[19] affy_1.32.0 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] affyio_1.22.0 Biostrings_2.22.0 IRanges_1.12.1
splines_2.14.0
[5] tools_2.14.0 zlibbioc_1.0.0
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