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