maigesRaw-class {maigesPack} | R Documentation

## maigesRaw class, store raw microarray datasets

### Description

This class describes objects to handle intensity values and information about genes and samples used in the data. Objects of this class are obtained from class `maigesPreRaw` using function `createMaigesRaw`.

### Details

This class of objects defines a real raw object that is used to do the normalisation. Objects of this class are generated from objects of class `maigesPreRaw` using the function `createMaigesRaw`. Here it is possible to do several plots for exploratory analysis using functions from marray package. Using the function `selSpots`, you select spots to use in the normalisation method, that is done by the functions `normLoc`, `normOLIN`, `normRepLoess`, `normScaleLimma` and `normScaleMarray`.

### Slots

`Sf`:
  numeric matrix containing the test samples spots intensity values, spots corresponding to rows and data tables (or chips) corresponding to columns.
`Sb`:
  numeric matrix containing the test samples local background values, spots corresponding to rows and data tables (or chips) corresponding to columns.
`Sdye`:
  character vector with length equal the length of data files (chips), specifying the channel ('ch1' or 'ch2') used to label each test sample in each chip.
`Rf`:
  numeric matrix containing the reference samples spots intensity values, spots corresponding to rows and data tables (or chips) corresponding to columns.
`Rf`:
  numeric matrix containing the reference samples spots intensity values, spots corresponding to rows and data tables (or chips) corresponding to columns.
`Rdye`:
  character vector with length equal the length of data files (chips), specifying the channel ('ch1' or 'ch2') used to label each reference sample in each chip.
`Flag`:
  matrix specifying the flags for the spots, as in the matrices above, rows and columns correspond to genes and samples, respectively. Type o value may be numeric or character, depending of the flags used.
`BadSpots`:
  logical vector specifying spots that was judged as bad ones. By default this slot is created as a vector of FALSEs with same length as number of spots.
`UseSpots`:
  logical matrix indexing the spots to be used for normalisation.
`GeneGrps`:
  a logical matrix with rows representing the spots and columns representing different gene groups. Each column give the index of spots in that gene group.
`Paths`:
  list containing `graphNEL` objects specifying gene regulatory networks (or pathways). The first object in this list is a char string giving the gene label used to match the genes.
`Layout`:
  a list containing the number of rows (`gridR`) and columns (`gridC`) of grids, the number of rows (`spotR`) and columns (`spotC`) of spots inside each grid and the total number of spots.
`Glabels`:
  data frame giving the gene labels. These labels are generally used during the data analysis.
`Slabels`:
  data frame giving the sample labels. These labels are generally used during the data analysis.
`Notes`:
  char string that receives any comment about the dataset. The dataset description is stored in this slot.
`Date`:
  char string giving the date and hour that the object was created.
`V.info`:
  list containg three characters. The first one is a string containing the R version used when the object was created. The second is a char vector with base packages and the last one is another char vector with additional packages and version numbers.

### Methods

[
  `signature(x = 'maigesRaw')`: subsetting operator for spots on the array or arrays in the batch, ensures that all slots are subset properly.
boxplot
  `signature(x = 'maigesRaw')`: boxplot method for `maigesRaw` class. Display boxplots of the slides and print tip groups using package marray.
dim
  `signature(x = 'maigesRaw', value = 'numeric')`: get the dimensions of the object, numeric vector of length two.
image
  `signature(x = 'maigesRaw')`: image method for `maigesRaw` class. Display colour representation of the slides using package marray.
plot
  `signature(x = 'maigesRaw')`: plot method for `maigesRaw` class. Display MA plots.
print
  `signature(x = 'maigesRaw')`: print method for `maigesRaw` class.
show
  `signature(x = 'maigesRaw')`: show method for `maigesRaw` class.
summary
  `signature(x = 'maigesRaw')`: summary method for `maigesRaw` class.

### Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

### See Also

`createMaigesRaw`, `selSpots`, `normLoc`, `normOLIN`, `normRepLoess`, `normScaleLimma` and `normScaleMarray`.

[Package maigesPack version 1.2.1 Index]