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illumina的450K芯片的beta值含义及计算方法

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发表于 2017-6-2 11:31:22 | 显示全部楼层 |阅读模式
illumina的软件(Illumina GenomeStudio Software)自动就把450k芯片的IDAT原始文件转换成了甲基化信号文件,一般是3~8列值每个样本。
A beta value was calculated for each CpG target with Illumina's Bead Studio software with the Methylation Module v3.2.
Beta-value = intensity value from the methylated bead type/(intensity values from the methylated + intensity value from unmethylated bead types + 100).
The data was then quality-filtered using p-values.
Beta values with p-value greater than 0.01 are considered to fall below the minimum intensity and threshold are displayed as "NA".


minfi包的一个函数read.450k.exp也可以直接读取 .IDAT files
(average β = signal B/(signal A + signal B + 100))
DNA methylation levels (β-values) were determined by calculating the ratio of intensities between methylated (signal A) and unmethylated (signal B) alleles.
Specifically, the β-value was calculated from the intensity of the methylated (M corresponding to signal A) and unmethylated (U corresponding to signal B) alleles, as the ratio of fluorescent signals β = Max(M,0)/[Max(M,0) + Max(U,0) + 100].
Thus, β-values range from 0 (completely unmethylated) to 1 (completely methylated)


具体beta值的意义是:
Any beta value equal to or greater than 0.6 was considered fully methylated.
Any beta value equal to or less than 0.2 was considered to be fully unmethylated.
Beta values between 0.2 and 0.6 were considered to be partially methylated.



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