| 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:Sb:Sdye:Rf:Rf:Rdye:Flag:BadSpots:UseSpots:GeneGrps:Paths: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: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:Slabels:Notes:Date:V.info: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.