This class describes objects to handle ratio of intensities (W)
and average of intensities (A) values values and information
about genes and samples used in the data. Objects of this class are
created from class
maigesRaw using the functions
normScaleMarray to do the normalisation.
Here, the M=log(R/G) value of intensity ratio was redefined as W=log(Test/Ref), where Test and Ref are the test and reference samples.
This defines the main class of objects defined in
this package. It is created from
using the normalisation functions
normScaleMarray. From this class
of objects it is possible to do any type of analysis defined by
several functions in this package. Also, it is possible to summarise
spots (or samples) information using the function
numeric matrix containing the ratio values (in log2 scale) between the test and reference sample intensities (W values). Spots are indexed by rows and samples by columns.
numeric matrix containing the mean intensity values between test and reference samples (also in log2 scale). Spots corresponding to rows and samples (or chips) corresponding to columns, too.
numeric matrix containing the standard deviation of W values when the lowess step is repeated several times.
numeric matrix containing the left margin of confidence interval defined by repeated lowess during the normalisation step.
numeric matrix containing the right margin of confidence interval defined above.
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.
logical matrix indexing the spots to be used for normalisation.
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.
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.
a list containing the number of rows (
gridC) of grids, the number of rows (
and columns (
spotC) of spots inside each grid and the total
number of spots.
data frame giving the gene labels. These labels are generally used during the data analysis.
data frame giving the sample labels. These labels are generally used during the data analysis.
char string that receives any comment about the dataset. The dataset description is stored in this slot.
char string giving the date and hour that the object was created.
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 = 'maiges'): subsetting operator for
spots on the array or arrays in the batch, ensures that all slots
are subset properly.
signature(x = 'maiges'): boxplot method for
maiges class. Display boxplots of the slides and
print tip groups using package marray or boxplots of
one gene previously defined.
signature(x = 'maiges', value = 'numeric'): get
the dimensions of the object, numeric vector of length two.
signature(x = 'maiges'): image method for
maiges class. Display colour representation of
the slides using package marray.
signature(x = 'maiges'): plot method for
maiges class. Display 'MA' plots.
signature(x = 'maiges'): print method for
signature(x = 'maiges'): show method for
signature(x = 'maiges'): summary method for
Gustavo H. Esteves <firstname.lastname@example.org>
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