[BioC] CNV detection using cn.farms for non-affymetrix arrays (custom oligonucleotide arrays)

Joan [guest] guest at bioconductor.org
Tue Apr 8 08:42:52 CEST 2014


I am interested in using the package for CNV detection from custom oligo array data (with probe names,locations, log2ratios and intensity data). From the paper, it is indicated that data from other platforms can be used as input, but the first analysis step i.e normalization takes only Cel files as input.

I have used cn.mops for WGS analysis and would like to compare results from sequencing and microarray using the same analytic approach.



 -- output of sessionInfo(): 

R version 3.0.3 (2014-03-06)
Platform: i386-w64-mingw32/i386 (32-bit)

[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] tools     parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] cn.farms_1.10.0      snow_0.3-13          oligoClasses_1.24.0 
[4] ff_2.2-12            bit_1.1-11           Biobase_2.22.0      
[7] BiocGenerics_0.8.0   BiocInstaller_1.12.0

loaded via a namespace (and not attached):
 [1] affxparser_1.34.2     affyio_1.30.0         Biostrings_2.30.1    
 [4] codetools_0.2-8       DBI_0.2-7             DNAcopy_1.36.0       
 [7] foreach_1.4.1         GenomicRanges_1.14.4  grid_3.0.3           
[10] IRanges_1.20.7        iterators_1.0.6       lattice_0.20-27      
[13] oligo_1.26.6          preprocessCore_1.24.0 splines_3.0.3        
[16] stats4_3.0.3          XVector_0.2.0         zlibbioc_1.8.0   

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