CNV detection using cn.farms for non-affymetrix arrays (custom oligonucleotide arrays)
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Guest User ★ 12k
@guest-user-4897
Last seen 7.1 years ago
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.
Sequencing Microarray probe cn.mops Sequencing Microarray probe cn.mops • 725 views
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Djork Clevert ▴ 210
@djork-clevert-422
Last seen 7.1 years ago
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-Arn? 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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