Illumina HM450 epigenetics

Question

[niutster]

Hi,

I have illumina 450 HM files in idat forms but there is some additional files such as "TableControl annotations HM450" and "TableControl data no normalisation HM450" but i dont know usage of them.

Thanks.

Answer 1

[andrew.j.skelton73]

Take your IDAT files, and follow the guide of a tool such as minfi

[niutster]

I need to know what are these files ,"Table Control...",... In the minfi package, there is not any information about these files.

[andrew.j.skelton73]

I imagine they're control probe information, information on hybridisation efficiency, bisulphide conversion, etc. You don't need to use them, the IDAT files are the truly raw data from the scanner, and it's what pipelines such as Minfi use as inputs.