targets {Agi4x44PreProcess} | R Documentation

## Example of target file

### Description

Example of target file

### Usage

    data(targets)

### Format

A data frame with 4 observations on the following 5 variables.

`FileName`
  names of the Files `Ast.txt` `Bst.txt` `Aunst.txt` `Bunst.txt`
`Treatment`
  Assigns level for Treatment Effect to each File (mandatory)
`GErep`
  a numeric vector tha numerates the FACTOR of the Treatment Effect (mandatory)
`Subject`
  Assigns level for Subject Effect to each file (optional)
`Array`
  Assigns level for Array Effect to each file (optional)

### Details

It is a tab-delimited text format file. The target file is created with the intention of carrying out a differential expression analysis in future steps using 'limma'. Therefore, here is where factors that are going to be included in the linear model that is fitted to each gen are specified. Targets file assigns each image data file to one of the experimental conditions of the experiment. First column 'FileName' is mandatory and includes image data files names. Second column 'Treatment' is also mandatory and includes treament effect. Third column 'GErep' is also mandatory, and includes the Treatment effect in a numeric code, from 1 to n, being n the number of Treatment effect levels. The rest of the columns are optional, and they can include other factors that we want to specify in the model, such as 'Subject', 'Array', and so on.

### References

Gordon K. Smyth, M. Ritchie, N. Thorne, J. Wettenhall (2007). limma: Linear Models for Microarray Data User's Guide.

### Examples

    ## Not run:
            data(targets)
    ## End(Not run)

[Package Agi4x44PreProcess version 1.4.0 Index]