CRLMM Annotation file
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@venu-pullabhatla-5550
Last seen 8.0 years ago
Hi All I am working on Illumina HumanOmni5MExome-4v1-1_A SNP array to identify CNV's and LOH's from this data. I have come across "crlmm" package that can do this and started following the "Preprocessing and Genotyping Illumina Arrays for Copy Number Analysis" vignette. I realized that the crlmm package does not include CDF annotation for this Illumina array. I tried to find this on the Bioconductor site and did not succeed. Can anyone please help me where I can find this annotation file or a way I can prepare one myself. Any help is very much appreciated. Many thanks. Venu
SNP Annotation cdf SNP Annotation cdf • 1.9k views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
Hi Venu, The crlmm package is intended for Affymetrix arrays, not Illumina. I believe you want the beadArraySNP package. Best, Jim On Wednesday, February 26, 2014 12:37:06 PM, Venu Pullabhatla wrote: > Hi All > > I am working on Illumina HumanOmni5MExome-4v1-1_A SNP array to > identify CNV's and LOH's from this data. I have come across "crlmm" > package that can do this and started following the "Preprocessing and > Genotyping Illumina Arrays for Copy Number Analysis" vignette. I > realized that the crlmm package does not include CDF annotation for > this Illumina array. I tried to find this on the Bioconductor site and > did not succeed. Can anyone please help me where I can find this > annotation file or a way I can prepare one myself. Any help is very > much appreciated. Many thanks. > > Venu > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi Jim Many thanks for your prompt response. I am surprised to know about crlmm specificity to Affymetrix because the vignette claims to be applicable for Illumina platforms also. I am referring to the following vignette. http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst /doc/IlluminaPreprocessCN.pdf I have come across beadArraySNP package, but if I am correct, this package needs text files imported from Genome Studio software. Can you please suggest any other package(s) that could read raw IDAT files perform CNV and LOH analysis. Many thanks. Best wishes Venu On 26/02/14 17:42, James W. MacDonald wrote: > Hi Venu, > > The crlmm package is intended for Affymetrix arrays, not Illumina. I > believe you want the beadArraySNP package. > > Best, > > Jim > > > > On Wednesday, February 26, 2014 12:37:06 PM, Venu Pullabhatla wrote: >> Hi All >> >> I am working on Illumina HumanOmni5MExome-4v1-1_A SNP array to >> identify CNV's and LOH's from this data. I have come across "crlmm" >> package that can do this and started following the "Preprocessing and >> Genotyping Illumina Arrays for Copy Number Analysis" vignette. I >> realized that the crlmm package does not include CDF annotation for >> this Illumina array. I tried to find this on the Bioconductor site and >> did not succeed. Can anyone please help me where I can find this >> annotation file or a way I can prepare one myself. Any help is very >> much appreciated. Many thanks. >> >> Venu >> >> _______________________________________________ >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 -- Venu Pullabhatla, Ph.D. Senior Bioinformatician NIHR GSTFT/KCL Comprehensive Biomedical Research Centre Guy's & St. Thomas' NHS Foundation Trust Guy's Hospital, Tower Wing, 16th Floor Great Maze Pond, London SE1 9RT Phone: 0044(0)2071887188 (x53378)
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Hi Venu, My bad! Looks like crlmm works for the Illumina platform as well. I guess that shows how long it's been since I did any SNP work... Best, Jim On 2/26/2014 12:53 PM, Venu Pullabhatla wrote: > Hi Jim > > Many thanks for your prompt response. I am surprised to know about > crlmm specificity to Affymetrix because the vignette claims to be > applicable for Illumina platforms also. I am referring to the > following vignette. > > http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/in st/doc/IlluminaPreprocessCN.pdf > > > I have come across beadArraySNP package, but if I am correct, this > package needs text files imported from Genome Studio software. Can you > please suggest any other package(s) that could read raw IDAT files > perform CNV and LOH analysis. Many thanks. > > Best wishes > > Venu > > On 26/02/14 17:42, James W. MacDonald wrote: >> Hi Venu, >> >> The crlmm package is intended for Affymetrix arrays, not Illumina. I >> believe you want the beadArraySNP package. >> >> Best, >> >> Jim >> >> >> >> On Wednesday, February 26, 2014 12:37:06 PM, Venu Pullabhatla wrote: >>> Hi All >>> >>> I am working on Illumina HumanOmni5MExome-4v1-1_A SNP array to >>> identify CNV's and LOH's from this data. I have come across "crlmm" >>> package that can do this and started following the "Preprocessing and >>> Genotyping Illumina Arrays for Copy Number Analysis" vignette. I >>> realized that the crlmm package does not include CDF annotation for >>> this Illumina array. I tried to find this on the Bioconductor site and >>> did not succeed. Can anyone please help me where I can find this >>> annotation file or a way I can prepare one myself. Any help is very >>> much appreciated. Many thanks. >>> >>> Venu >>> >>> _______________________________________________ >>> 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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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