limma (version 3.28.6)

read.idat: Read Illumina expression data directly from IDAT files

Description

Read Illumina BeadArray data from IDAT and manifest (.bgx) files for gene expression platforms.

Usage

read.idat(idatfiles, bgxfile, dateinfo=FALSE, tolerance=0)

Arguments

idatfiles

character vector specifying idat files to be read in.

bgxfile

character string specifying bead manifest file (.bgx) to be read in.

dateinfo

logical. Should date and software version info be read in?

tolerance

numeric. The number of probe ID discrepancies allowed between the manifest and a given idat file.

Value

• An EListRaw-class object with the following components:
• E
  numeric matrix of raw intensities.
• other
  list containing matrices of NumBeads and STDEV for each probe.
• genes
  data.frame of probe annotation.
• targets
  data.frame of sample information.

concept

• illumina microarrays
• microarray data file

Details

Illumina's BeadScan/iScan software ouputs probe intensities in IDAT format (encrypted XML files) and probe info in a platform specific manifest file (.bgx). These files can be processed using the low-level functions readIDAT and readBGX from the illuminaio package (Smith et al. 2013).

The read.idat function provides a convenient way to read these files. into R and store them in an EListRaw-class object (similar to read.ilmn, which imports data output by Illumina's GenomeStudio software) that can be used by downstream processing functions in limma.

Probe types are indicated in the Status column of the genes component of the EListRaw-class object.

References

Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD (2013). illuminaio: An open source IDAT parsing tool. F1000 Research 2, 264. http://f1000research.com/articles/2-264/v1

See Also

read.ilmn imports gene expression data output by GenomeStudio.

neqc performs normexp by control background correction, log transformation and quantile between-array normalization for Illumina expression data.

propexpr estimates the proportion of expressed probes in a microarray.

Examples

idatfiles = dir(pattern="idat")
bgxfile = dir(pattern="bgx")
data = read.idat(idatfiles, bgxfile)
propexpr(data)
datanorm = neqc(data)