Removing Illumina microarray probes with no expression HumanHT-12v4

Question

[Bioinformatician]

I am analyzing a microarray data set generated with Illumina HumanHT-12v4. I have files with the idat extension and use the "read.idat" function in limma to read the raw microarray data into an EListRaw. I am trying to remove probes with very low expression and don't see a straight path to doing it.

The Limma user guide recommends the following command to filter out low expression probes:

expressed <- rowSums(y$other$Detection < 0.05) >= 3
y <- y[expressed,]

The ElistRaw object only has NumBeads and STDEV under y$other. Any suggestions to remove low expression probes?

Answer 1

[Gordon Smyth]

Type

help("read.idat")

and read the example at the bottom of the page, which shows you how to set the other$Detection component of the EListRaw object. Alternatively, you could just type example(read.idat).

Questions so that are so specific to limma are best sent to the Bioconductor support site. See "How to get help" in the limma User's Guide.