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. The `MIAME` class is derived from `MIAxE`.

### 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` containing 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

Constructor methods:

`MIAME()`:

  `MIAME(name = "", lab = "", contact = "", title = "", abstract = "", url = "", pubMedIds = "" , samples = "", hybridizations = list(), normControls = list(), preprocessing = list(), other = list())`: Creates a new `MIAME` object with slots as defined above.

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 2.40.0 Index]