RNA Sequencing Differential Expression with IDAT Files

Question

[questionaire]

Hello All:

I have a set of IDAT files with a sample layout manifest. I want to do differential expression on these files. Does anyone happen to know of any R packages that would help in doing so? Thank you in advance.

Answer 1

[andrew.j.skelton73]

I'm assuming these are gene expression arrays, rather than RNA sequencing. Typically if you have IDAT files, you need to use GenomeStudio (proprietary software sold by Illumina), to create an experiment sample probe profile, and control probe profile. There are alternatives to that route in LumIdat which basically calls a Java jar file that provides an IDAT to probe profile utility. Alternatively Limma offers a read.idat function, and if you check the documentation, there's a nice walkthrough from IDATs to neqc normalised data.

From the read.idat function:

idatfiles <- dir(pattern="idat")
bgxfile   <- dir(pattern="bgx")
x         <- read.idat(idatfiles, bgxfile)
x$other$Detection <- detectionPValues(x)
propexpr(data)
y <- neqc(data)

Note that the bgx file it's referring to can be found on the Illumina website for the respective platform you're working with.