maigesRaw-class: maigesRaw class, store raw microarray datasets

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

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.

Rb:

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 <[e-mail]>

See Also

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

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.