Question: CNV detection using cn.farms for non-affymetrix arrays (custom oligonucleotide arrays)
5.7 years ago by
Guest User • 12k
Guest User • 12k wrote:
Hi, 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. Thanks Joan -- output of sessionInfo(): R version 3.0.3 (2014-03-06) Platform: i386-w64-mingw32/i386 (32-bit) locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  tools parallel stats graphics grDevices utils datasets  methods base other attached packages:  cn.farms_1.10.0 snow_0.3-13 oligoClasses_1.24.0  ff_2.2-12 bit_1.1-11 Biobase_2.22.0  BiocGenerics_0.8.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached):  affxparser_1.34.2 affyio_1.30.0 Biostrings_2.30.1  codetools_0.2-8 DBI_0.2-7 DNAcopy_1.36.0  foreach_1.4.1 GenomicRanges_1.14.4 grid_3.0.3  IRanges_1.20.7 iterators_1.0.6 lattice_0.20-27  oligo_1.26.6 preprocessCore_1.24.0 splines_3.0.3  stats4_3.0.3 XVector_0.2.0 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
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