readHeader {limma} | R Documentation

## Read Header Information from Microarray Raw Data File

### Description

Read the header information from a microarray raw data file, as output from an image analysis software program such as GenePix. These functions are used internally by `read.maimages` and are not usually called directly by users.

### Usage

    readGenericHeader(file, columns, sep="\t")
    readGPRHeader(file)
    readSMDHeader(file)

### Arguments

`file` | character string giving file name. If it does not contain an absolute path, the file name is relative to the current working directory.
`columns` | character vector specifying data column headings expected to be in file
`sep` | the character string separating column names

### Details

Raw data files exported by image analysis programs include a number of header lines which contain information about the scanning process. This function extracts that information and locates the line where the intensity data begins. `readGPRHeader` is for GenePix output and `readSMDHeader` is for files from the Stanford Microarray Database (SMD). `readGenericHeader` finds the line in the file on which the data begins by searching for specified column headings.

### Value

A list with components corresponds to lines of header information. A key component is `NHeaderRecords` which gives the number of lines in the file before the intensity data begins. All other components are character vectors.

### Author(s)

Gordon Smyth

### References

See http://www.cryer.co.uk/file-types/a/atf/genepix_file_formats.htm for GenePix formats.

See http://smd.princeton.edu for the SMD.

### See Also

`read.maimages`

An overview of LIMMA functions to read data is given in 03.ReadingData.

[Package limma version 3.42.2 Index]