How to view TCGA data in idat format file.
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.
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Ashwini Patil •
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singhparisha •
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singhparisha •
2 answers
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)
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Ashwini Patil •
Should be easy to search in the internet. RnBeads , you can find the vigenette here
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ivivek_ngs
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