how to use idat file for analyses in bioconductor

Question

[Kritika]

Hello all,

I want to know how to use idat file for analysis in bioconductor.

I read certain packages manual (limma and lumi). There it is said for analyses I need .txt file which is generated from genome studio.

For my dummy sample I run the genome studio too. How I will get text files for analyses using lumi or limma

I also tried using illuminaio which only read idat

Is there any procedure in bioconductor which will convert idat to txt. Or it is obtained from genomestudio? if yes then how to get it from genome studio?

Also one more question is there any script which directly read idat file ? I tried one script which is giving me error.

Please help

Thank You

Answer 1

[Gordon Smyth]

The read.idat function in the limma package will read the idat files directly into an expression object.

Answer 2

[Giulio Genovese]

You can also use my bcftools plugin gtc2vcf with option --idat to see the content of an IDAT file in text format