How to view TCGA data in idat format file.

Question

[singhparisha]

I want to analyze the data of tcga on methylation, but I am having difficulty as the downloaded file is in idat format. Could anyone please suggest me how to open the file and by which software.

Answer 1

[Ashwini Patil]

You can use minfi R package (https://bioconductor.org/packages/3.3/bioc/manuals/minfi/man/minfi.pdf) to read and normalize idat files.

targets <- read.450k.sheet(baseDir)
sub(baseDir, "", targets$Basename)
RGset <- read.450k.exp(base = baseDir, targets = targets)

Answer 2

[ivivek_ngs]

Should be easy to search in the internet. RnBeads , you can find the vigenette here