read.ilmn {limma} | R Documentation

## Read Illumina Expression Data

### Description

Read Illumina summary probe profile files and summary control probe profile files

### Usage

    read.ilmn(files=NULL, ctrlfiles=NULL, path=NULL, ctrlpath=NULL, probeid="Probe",
              annotation=c("TargetID", "SYMBOL"), expr="AVG_Signal",
              other.columns="Detection", sep="\t", quote="\"", verbose=TRUE, ...)

### Arguments

`files` | character vector giving the names of the summary probe profile files.
`ctrlfiles` | character vector giving the names of the summary control probe profile files.
`path` | character string giving the directory containing the summary probe profile files. Default is the current working directory.
`ctrlpath` | character string giving the directory containing the summary control probe profile files. Default is the same directory as for the probe profile files.
`probeid` | character string giving the name of the probe identifier column.
`annotation` | character vector giving possible column names for probe annotation.
`expr` | character string giving a keyword identifying the expression intensity columns. Any input column with column name containing this key will be read as containing intensity values.
`other.columns` | character vector giving keywords sufficient to identify any extra data columns that should be read in, such as "Detection", "Avg_NBEADS", "BEAD_STDEV" etc. The default of `Detection` is usually sufficient to identify the columns containing detection p-values.
`sep` | the field separator character.
`quote` | character string of characters to be treated as quote marks.
`verbose` | logical, `TRUE` to report names of profile files being read.
`...` | any other parameters are passed on to `read.columns`.

### Details

Illumina BeadStudio ouputs probe intensities (regular probe intensities) and control probe intensities to summary probe profile files (containing regular probes) and summary control probe profile files, respectively. If both `files` and `ctrlfiles` are not `NULL`, this function will combine the data read from the two file types and save them to an `EListRaw-class` object. If one of them is `NULL`, then only the required data are read in.

Probe types are indicated in the `Status` column of `genes`, a component of the returned `EListRaw-class` object. There are totally seven types of control probes including `negative`, `biotin`, `labeling`, `cy3_hyb`, `housekeeping`, `high_stringency_hyb` or `low_stringency_hyb`. Regular probes have the probe type `regular`. The `Status` column will not be created if `ctrlfiles` is `NULL`.

To read in columns other than `probeid`, `annotation` and `expr`, users needs to specify keywords in `other.columns`. One keyword corresponds to one type of columns. Examples of keywords are "Detection", "Avg_NBEADS", "BEAD_STDEV" etc.

### Value

An `EListRaw-class` object with the following components:

`E` | numeric matrix of intensities.
`genes` | data.frame of probe annotation. Contains any columns specified by `annotation` that are found in the input files.
`other` | a list of matrices corresponding to any `other.columns` found in the input files.

### Author(s)

Wei Shi and Gordon K Smyth

### See Also

`read.ilmn.targets` reads in Illumina expression data using the file information extracted from a target data frame which is often created by the `readTargets` function.

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

`normexp.fit.control` estimates the parameters of the normal+exponential convolution model with the help of negative control probes.

`propexpr` estimates the proportion of expressed probes in a microarray.

### Examples

    ## Not run:
    x <- read.ilmn(files="sample probe profile.txt",
                   ctrlfiles="control probe profile.txt")

    ## End(Not run)
    # See neqc and beadCountWeights for other examples using read.ilmn

[Package limma version 3.38.3 Index]