| read.idat {limma} | R Documentation |
Read Illumina BeadArray data from IDAT and manifest (.bgx) files for gene expression platforms.
read.idat(idatfiles, bgxfile, dateinfo=FALSE, tolerance=0)
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. |
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.
An EListRaw-class object with the following components:
E |
numeric matrix of raw intensities. |
other |
list containing matrices of |
genes |
data.frame of probe annotation. |
targets |
data.frame of sample information. |
Matt Ritchie
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
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.
## Not run: idatfiles = dir(pattern="idat") bgxfile = dir(pattern="bgx") data = read.idat(idatfiles, bgxfile) propexpr(data) datanorm = neqc(data) ## End(Not run)