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用R包crlmm来分析Affymetrix SNP 5.0 and 6.0 and Illumina arrays

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发表于 2017-2-14 11:31:14 | 显示全部楼层 |阅读模式
反正就是分析affymetrix的SNP5.0或者6.0拷贝数变异芯片啦!
http://bioconductor.org/packages/release/bioc/html/crlmm.html

当然,还可以分析illumina的基因型芯片:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752620/
For Infinium genotyping, beads are coupled with specific 50mer probes designed to be complementary to the sequence adjacent to the SNP site, and the two alleles (A, B) are discriminated using either a red or green dye


PDFCopy number estimation
PDFcrlmm Vignette - Downstream Analysis
PDFR Scriptcrlmm Vignette - Genotyping
PDFInfrastructure for copy number analysis
PDFOverview of copy number vignettes
PDFPreprocessing and genotyping Illumina arrays for copy number analysis
PDF Reference Manual
Text NEWS



也可以直接去读取IDAT文件,需要熟悉这个包即可!
To begin, summarized data are read from idat files (two per array, one for each channel) using the function readIdatFiles.
Binary idat files are a convenient starting point, as they are routinely output by the scanning software, provide a compact representation of the data and have a consistent format (unlike output from Illumina's BeadStudio/GenomeStudio software, which is exported at the user's discretion, meaning the raw signals needed for the analysis are not always available).










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你这个问题很复杂,需要打赏,请点击 http://www.bio-info-trainee.com/donate 进行打赏,谢谢
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