maigesRaw-class {maigesPack} | R Documentation |
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
.
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
.
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.
signature(x = 'maigesRaw')
: subsetting operator for
spots on the array or arrays in the batch, ensures that all slots
are subset properly.
signature(x = 'maigesRaw')
: boxplot method for
maigesRaw
class. Display boxplots of the slides and
print tip groups using package marray.
signature(x = 'maigesRaw', value = 'numeric')
: get
the dimensions of the object, numeric vector of length two.
signature(x = 'maigesRaw')
: image method for
maigesRaw
class. Display colour representation of
the slides using package marray.
signature(x = 'maigesRaw')
: plot method for
maigesRaw
class. Display MA plots.
signature(x = 'maigesRaw')
: print method for
maigesRaw
class.
signature(x = 'maigesRaw')
: show method for
maigesRaw
class.
signature(x = 'maigesRaw')
: summary method for
maigesRaw
class.
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
createMaigesRaw
, selSpots
,
normLoc
, normOLIN
,
normRepLoess
, normScaleLimma
and
normScaleMarray
.