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illumina芯片的raw signal intensity data from the *.idat files

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发表于 2017-2-18 10:15:57 | 显示全部楼层 |阅读模式
通常是illumina公司出品的芯片才会给idat格式的文件:
The IDAT file format is used to store BeadArray data from the myriad of genomewide profiling platforms on offer from Illumina Inc.
This proprietary format is output directly from the scanner and stores summary intensities for each probe-type on an array in a compact manner.
A lack of open source tools to process IDAT files has hampered their uptake by the research community beyond the standard step of using the vendor’s software to extract the data they contain in a human readable text format.
需要转换成人类可以阅读的文本格式文件:
比如这个Illumina Infinium Omni5Exome-4 Kit数据:
https://www.encodeproject.org/experiments/ENCSR112SHO/
下载下来就是idat格式,但是我们需要的是基因型文本文件。
中间需要转换,我本来准备用illumina公司出品的genomestudio软件,但是没有找到方法。
https://www.illumina.com/content ... lysis_workflows.pdf

所以搜索到了R包:illuminaio
https://f1000research.com/articles/2-264/v1

既然是R包,就非常简单啦,阅读说明书即可
https://bioconductor.org/package ... tml/illuminaio.html



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