Question: Question on copy number estimation for Affymetrix SNP array 100k and 500k
0
gravatar for Julie Zhu
9.2 years ago by
Julie Zhu4.1k
United States
Julie Zhu4.1k wrote:
Hi, The crlmm package implements copy number estimation for Affymetrix SNP 6.0 platform. The genoCN package has functions for identification of copy number states for Illumina SNP array. I am wondering how I could adopt crlmm package or geneoCN package to estimate copy number for the old Affymetrix SNP platforms (100k and 500k) using CEL files as input. I also tried aroma.Affymetrix and aroma.cn but encountered the following error even though the directory Nsp_CEL_CML does contain the CEL files with chip type of Mapping250K_Nsp. Thank you very much for your help! Best regards, Julie library(aroma.affymetrix) libraryaroma.cn) cs <- AffymetrixCelSet$byName("Nsp_CEL_CML", chipType="Mapping250K_Nsp") Error in list(`AffymetrixCelSet$byName("Nsp_CEL_CML", chipType = "Mapping250K_Nsp")` = <environment>, : [2010-09-20 17:21:12] Exception: Could not locate a file for this chip type: Mapping250K_Nsp at throw(Exception(...)) at throw.default("Could not locate a file for this chip type: ", paste(c(chipType, tags), at throw("Could not locate a file for this chip type: ", paste(c(chipType, tags), collaps at method(static, ...) at AffymetrixCdfFile$byChipType(chipType) at method(static, ...) at AffymetrixCelSet$byName("Nsp_CEL_CML", chipType = "Mapping250K_Nsp") > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] geneplotter_1.26.0 lattice_0.18-8 annotate_1.26.1 [4] AnnotationDbi_1.10.2 pd.mapping250k.nsp_1.0.0 RSQLite_0.9-2 [7] DBI_0.2-5 aroma.cn_0.5.0 aroma.affymetrix_1.7.0 [10] aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0 [13] aroma.core_1.7.0 aroma.light_1.16.1 matrixStats_0.2.1 [16] R.rsp_0.4.0 R.cache_0.3.0 R.filesets_0.9.0 [19] digest_0.4.2 R.utils_1.5.2 R.oo_1.7.3 [22] oligo_1.12.2 R.methodsS3_1.2.0 VanillaICE_1.10.0 [25] IRanges_1.6.11 crlmm_1.6.5 oligoClasses_1.10.0 [28] Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 Biostrings_2.16.9 bit_1.1-4 [4] ellipse_0.3-5 ff_2.1-2 genefilter_1.30.0 [7] grid_2.11.1 KernSmooth_2.23-3 mvtnorm_0.9-92 [10] preprocessCore_1.10.0 RColorBrewer_1.0-2 splines_2.11.1 [13] survival_2.35-8 tools_2.11.1 xtable_1.5-6
snp crlmm genocn • 735 views
ADD COMMENTlink modified 9.2 years ago by Henrik Bengtsson2.4k • written 9.2 years ago by Julie Zhu4.1k
Answer: Question on copy number estimation for Affymetrix SNP array 100k and 500k
0
gravatar for Henrik Bengtsson
9.2 years ago by
United States
Henrik Bengtsson2.4k wrote:
Hi, regarding your question on aroma.affymetrix; The aroma.* framework use a well-defined an strict directory and filename convention for locating data file sets and annotation data files. It seems to me that you haven't placed the CDF for your chip type in the correct directory. This is all explained at http://www.aroma-project.org/ under the 'Get started' section (and subsection 'Setup'). For future questions related to aroma.affymetrix, please use its dedicated mailing list/forum; http://www.aroma-project.org/forum/ Hope this helps /Henrik On Mon, Sep 20, 2010 at 3:27 PM, Zhu, Julie <julie.zhu at="" umassmed.edu=""> wrote: > Hi, > > The crlmm package implements copy number estimation for Affymetrix SNP 6.0 > platform. The genoCN package has functions for identification of copy number > states for Illumina SNP array. > > I am wondering how I could adopt crlmm package or geneoCN package to > estimate copy number for the old Affymetrix SNP platforms (100k and 500k) > using CEL files as input. > > I also tried aroma.Affymetrix and aroma.cn but encountered the following > error even though the directory Nsp_CEL_CML does contain the CEL files with > chip type of Mapping250K_Nsp. > > Thank you very much for your help! > > Best regards, > > Julie > > library(aroma.affymetrix) > libraryaroma.cn) > cs <- AffymetrixCelSet$byName("Nsp_CEL_CML", chipType="Mapping250K_Nsp") > Error in list(`AffymetrixCelSet$byName("Nsp_CEL_CML", chipType = > "Mapping250K_Nsp")` = <environment>, ?: > > [2010-09-20 17:21:12] Exception: Could not locate a file for this chip type: > Mapping250K_Nsp > ?at throw(Exception(...)) > ?at throw.default("Could not locate a file for this chip type: ", > paste(c(chipType, tags), > ?at throw("Could not locate a file for this chip type: ", paste(c(chipType, > tags), collaps > ?at method(static, ...) > ?at AffymetrixCdfFile$byChipType(chipType) > ?at method(static, ...) > ?at AffymetrixCelSet$byName("Nsp_CEL_CML", chipType = "Mapping250K_Nsp") > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > ?[1] geneplotter_1.26.0 ? ? ? lattice_0.18-8 ? ? ? ? ? annotate_1.26.1 > ?[4] AnnotationDbi_1.10.2 ? ? pd.mapping250k.nsp_1.0.0 RSQLite_0.9-2 > ?[7] DBI_0.2-5 ? ? ? ? ? ? ? ?aroma.cn_0.5.0 > aroma.affymetrix_1.7.0 > [10] aroma.apd_0.1.7 ? ? ? ? ?affxparser_1.20.0 ? ? ? ?R.huge_0.2.0 > [13] aroma.core_1.7.0 ? ? ? ? aroma.light_1.16.1 ? ? ? matrixStats_0.2.1 > [16] R.rsp_0.4.0 ? ? ? ? ? ? ?R.cache_0.3.0 ? ? ? ? ? ?R.filesets_0.9.0 > [19] digest_0.4.2 ? ? ? ? ? ? R.utils_1.5.2 ? ? ? ? ? ?R.oo_1.7.3 > [22] oligo_1.12.2 ? ? ? ? ? ? R.methodsS3_1.2.0 ? ? ? ?VanillaICE_1.10.0 > [25] IRanges_1.6.11 ? ? ? ? ? crlmm_1.6.5 ? ? ? ? ? ? ?oligoClasses_1.10.0 > [28] Biobase_2.8.0 > > loaded via a namespace (and not attached): > ?[1] affyio_1.16.0 ? ? ? ? Biostrings_2.16.9 ? ? bit_1.1-4 > ?[4] ellipse_0.3-5 ? ? ? ? ff_2.1-2 ? ? ? ? ? ? ?genefilter_1.30.0 > ?[7] grid_2.11.1 ? ? ? ? ? KernSmooth_2.23-3 ? ? mvtnorm_0.9-92 > [10] preprocessCore_1.10.0 RColorBrewer_1.0-2 ? ?splines_2.11.1 > [13] survival_2.35-8 ? ? ? tools_2.11.1 ? ? ? ? ?xtable_1.5-6 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 9.2 years ago by Henrik Bengtsson2.4k
Hi Henrik, Thank you very much for the quick response and the link! Best regards, Julie ________________________________________ From: henrik.bengtsson@gmail.com [henrik.bengtsson@gmail.com] On Behalf Of Henrik Bengtsson [hb@stat.berkeley.edu] Sent: Monday, September 20, 2010 8:30 PM To: Zhu, Julie Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Question on copy number estimation for Affymetrix SNP array 100k and 500k Hi, regarding your question on aroma.affymetrix; The aroma.* framework use a well-defined an strict directory and filename convention for locating data file sets and annotation data files. It seems to me that you haven't placed the CDF for your chip type in the correct directory. This is all explained at http://www.aroma-project.org/ under the 'Get started' section (and subsection 'Setup'). For future questions related to aroma.affymetrix, please use its dedicated mailing list/forum; http://www.aroma-project.org/forum/ Hope this helps /Henrik On Mon, Sep 20, 2010 at 3:27 PM, Zhu, Julie <julie.zhu at="" umassmed.edu=""> wrote: > Hi, > > The crlmm package implements copy number estimation for Affymetrix SNP 6.0 > platform. The genoCN package has functions for identification of copy number > states for Illumina SNP array. > > I am wondering how I could adopt crlmm package or geneoCN package to > estimate copy number for the old Affymetrix SNP platforms (100k and 500k) > using CEL files as input. > > I also tried aroma.Affymetrix and aroma.cn but encountered the following > error even though the directory Nsp_CEL_CML does contain the CEL files with > chip type of Mapping250K_Nsp. > > Thank you very much for your help! > > Best regards, > > Julie > > library(aroma.affymetrix) > libraryaroma.cn) > cs <- AffymetrixCelSet$byName("Nsp_CEL_CML", chipType="Mapping250K_Nsp") > Error in list(`AffymetrixCelSet$byName("Nsp_CEL_CML", chipType = > "Mapping250K_Nsp")` = <environment>, : > > [2010-09-20 17:21:12] Exception: Could not locate a file for this chip type: > Mapping250K_Nsp > at throw(Exception(...)) > at throw.default("Could not locate a file for this chip type: ", > paste(c(chipType, tags), > at throw("Could not locate a file for this chip type: ", paste(c(chipType, > tags), collaps > at method(static, ...) > at AffymetrixCdfFile$byChipType(chipType) > at method(static, ...) > at AffymetrixCelSet$byName("Nsp_CEL_CML", chipType = "Mapping250K_Nsp") > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] geneplotter_1.26.0 lattice_0.18-8 annotate_1.26.1 > [4] AnnotationDbi_1.10.2 pd.mapping250k.nsp_1.0.0 RSQLite_0.9-2 > [7] DBI_0.2-5 aroma.cn_0.5.0 > aroma.affymetrix_1.7.0 > [10] aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0 > [13] aroma.core_1.7.0 aroma.light_1.16.1 matrixStats_0.2.1 > [16] R.rsp_0.4.0 R.cache_0.3.0 R.filesets_0.9.0 > [19] digest_0.4.2 R.utils_1.5.2 R.oo_1.7.3 > [22] oligo_1.12.2 R.methodsS3_1.2.0 VanillaICE_1.10.0 > [25] IRanges_1.6.11 crlmm_1.6.5 oligoClasses_1.10.0 > [28] Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 Biostrings_2.16.9 bit_1.1-4 > [4] ellipse_0.3-5 ff_2.1-2 genefilter_1.30.0 > [7] grid_2.11.1 KernSmooth_2.23-3 mvtnorm_0.9-92 > [10] preprocessCore_1.10.0 RColorBrewer_1.0-2 splines_2.11.1 > [13] survival_2.35-8 tools_2.11.1 xtable_1.5-6 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 9.2 years ago by Julie Zhu4.1k
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