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

[Djork-Arné Clevert]

Hi Joan,

it’s very nice to read that you use our cn.MOPS-algortihm for detecting CNVs in NGS-data. 

However, just to make sure that we are in the same ballpark: 
cn.MOPS (Copy Number estimation by a Mixture Of PoissonS) and 
cn.FARMS (Copy Number Factor Analysis for Robust Microarray Summarization) 
are both latent variable models for detecting CNVs but apart from that they have 
nothing in common.

I have a version of our cn.farms algorithm that works well with Illumina and Agilent arrays, but
it's sad to say, this version is not well documented. I will make up for this omission, review 
the code and send you an R-script this evening or at latest tomorrow. 

Cheers,
Okko
 
-- 
Djork-Arné Clevert, PhD
Institute of Bioinformatics
Johannes Kepler University Linz

Phone: +49 30 6883 5306
Fax: +49 30 6883 5307
Email: okko at clevert.de

Am 08.04.2014 um 08:42 schrieb Joan [guest] <guest at bioconductor.org>:

> 
> 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:
> [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   
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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