MIAME {Biobase} | R Documentation

## Class for Storing Microarray Experiment Information

### Description

Class `MIAME` covers MIAME entries that are not covered by other classes in Bioconductor. Namely, experimental design, samples, hybridizations, normalization controls, and pre-processing information.

### Slots

`name`:
  Object of class `character` containing the experimenter name
`lab`:
  Object of class `character` containing the laboratory where the experiment was conducted
`contact`:
  Object of class `character` containing contact information for lab and/or experimenter
`title`:
  Object of class `character` containing a single-sentence experiment title
`abstract`:
  Object of class `character` containing an abstract describing the experiment
`url`:
  Object of class `character` containing a URL for the experiment
`samples`:
  Object of class `list` containg information about the samples
`hybridizations`:
  Object of class `list` containing information about the hybridizations
`normControls`:
  Object of class `list` containing information about the controls such as house keeping genes
`preprocessing`:
  Object of class `list` containing information about the pre-processing steps used on the raw data from this experiment
`pubMedIds`:
  Object of class `character` listing strings of PubMed identifiers of papers relevant to the dataset
`other`:
  Object of class `list` containing other information for which none of the above slots does not applies

### Methods

Class-specific methods:

`abstract(MIAME)`:
  An accessor function for `abstract`.
`combine(MIAME,MIAME)`:
  Combine two objects of `MIAME-class`, issuing warnings when ambiguities encountered.
`expinfo(MIAME)`:
  An accessor function for `name`, `lab`, `contact`, `title`, and `url`.
`hybridizations(MIAME)`:
  An accessor function for `hybridizations`.
`normControls(MIAME)`:
  An accessor function for `normControls`.
`notes(MIAME), notes(MIAME) <- value`:
  Accessor functions for `other`. `notes(MIAME) <- character` appends character to notes; use `notes(MIAME) <- list` to replace the notes entirely.
`otherInfo(MIAME)`:
  An accessor function for `other`.
`preproc(MIAME)`:
  An accessor function for `preprocessing`.
`pubMedIds(MIAME), pubMedIds(MIAME) <- value`:
  Accessor function for `pubMedIds`.
`samples(MIAME)`:
  An accessor function for `samples`.

Standard generic methods:

`updateObject(object, ..., verbose=FALSE)`
  Update instance to current version, if necessary. See `updateObject`
`isCurrent(object)`
  Determine whether version of object is current. See `isCurrent`
`isVersioned(object)`
  Determine whether object contains a 'version' string describing its structure . See `isVersioned`
`show(MIAME)`:
  Renders information about the MIAME information

### Author(s)

Rafael A. Irizarry

### References

http://www.mged.org/Workgroups/MIAME/miame_1.1.html

### See Also

`class:characterORMIAME`, `read.MIAME`

[Package Biobase version 2.0.1 Index]