read.exprSet {Biobase} | R Documentation

## Read Experimental Data and into an 'exprSet' Object

### Description

An exprSet object has a slot named `exprs` for experimental data. `read.exprSet` reads the experimental data stored as a text file and then generates an exprSet object using the data. Data for other slots can be also read in as options.

### Usage

    read.exprSet(exprs, se.exprs, phenoData, annotation, description, notes, seps = "\t")

### Arguments

`exprs` | `exprs` a character string for the name of the text file that stores the experimental data to be read in. The text file is assumed to be a delimited file with observed expression levels arranged in rows and columns. The first row of the file is sample names and the first column is gene names/ids. The file will be read in using read.table with header set to TRUE
`se.exprs` | `se.exprs` a character stirng for the name of a delimited text file contains standard error estimates for the estimated expression in exprs. The file is of the same dimensions as 'exprs'
`phenoData` | `phenoData` a character string for the name of an optional file containing information for 'pData' slot of a phenoData object to be returned. If missing a default phenoData object with one covariate ranging from 1 to the number of columns of 'exprs' will be provided
`annotation` | `annotation` a character string for the name of an optional text file that contains a string identifying the annotation that may be used for the 'exprSet' instance
`description` | `description` a character string for the name of an optional file containing MIAME information
`notes` | `notes` a character string for the name of an optional text file containing explanatory text
`seps` | `seps` a vector of character strings defining the delimitors used by 'exprs' and 'se.exprs'. The length of 'seps' can be 1 when both file have the same delimiter or 'se.exprs' is missing or 2 other wise. The delimitor for 'exprs' is expected to be the first element

### Details

If not missing, 'phenoData' will be read in using `read.phenoData` and description using `read.MIAME`. The help files of the two functions contain detailed descriptions of the two functions.

### Value

This function returns an `exprSet` object.

### Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide bioinformatics functionalities through R

### Author(s)

Jianhua Zhang

### See Also

`exprSet`, `phenoData`, `MIAME`, `read.phenoData`, `read.MIAME`

### Examples

    # Creating a test data
    testFile <- tempfile()
    data(geneData)
    write.table(geneData, testFile, quote = FALSE, sep = "\t", row.names =
    TRUE, col.names = TRUE)
    # Create an exprSet object using textFile
    eSet <- read.exprSet(testFile)
    eSet

[Package Biobase version 1.12.2 Index]