exprSetArray-class {arrayMagic}R Documentation

Class exprSetArray, an extension for cDNA data of the class exprSet, which a class for microarray data, and methods for processing them

Description

This is class representation for cDNA Microarray Data

Creating Objects

new('exprSetArray',
channels = ..., # Object of class matrix with columns "Cy3" and "Cy5"
exprs = ..., # Object of class matrix
se.exprs = ..., # Object of class matrix
phenoData= ..., # Object of class phenoData
notes = ...., # Object of class character
)

Slots

indCy3:
Object of class "vector"; indexes of channel Cy3
indCy5:
Object of class "vector"; indexes of channel Cy5
exprs:
Object of class "matrix"; the observed expression levels. This is a matrix with columns representing channels Cy3 and Cy5, the pairs given in channels define slides and rows representing genes.
se.exprs:
Object of class "matrix"; this is a matrix of the same dimensions as exprs which contains standard error estimates for the estimated expression levels.
phenoData:
Object of class "phenoData" This is an instance of class phenoData containing channel annotations. The columns of the pData slot of this entity represent variables and the rows represent channels.
notes:
Object of class "character" Vector of explanatory text

Methods

show
(exprSetArray): renders information about the exprSetArray in a concise way on stdout, cf. exprSet
getExprSetDiff
(exprSetArray): Returns an exprSet object of the difference of the expression levels of channel Cy3 and channel Cy5. The se.exprs slot contains the sum of the se.exprs of both channels.
getExprSetCy3MinusCy5
same as getExprSetDiff
getExprSetCy3
(exprSetArray): Returns an exprSet object of the expression levels of channel Cy3
getExprSetCy5
(exprSetArray): Returns an exprSet object of the expression levels of channel Cy5
phenoDataSlide
(exprSetArray): Returns an phenoData object of the slides which contains those annotation information (variables), which are the same for both channels, e.g. the slide number - NAs are not taken into consideration.
pDataSlide
(exprSetArray): Returns an pData object of the slides which contains those annotation information (variables), which is the same for both channels, e.g. the slide number - NAs are not taken into consideration. Do not use varLabels-names for subsetting - only indexes.
phenoDataCy3
(exprSetArray): Returns an phenoData object of the annotation information given for channel Cy3. Do not use varLabels-names for subsetting - only indexes.
pDataCy3
(exprSetArray): Returns the pData object given by phenoDataCy3. Do not use varLabels-names for subsetting - only indexes.
phenoDataCy5
(exprSetArray): Returns an phenoData object of the annotation information given for channel Cy5. Do not use varLabels-names for subsetting - only indexes.
pDataCy5
(exprSetArray): Returns the pData object given by phenoDataCy5. Do not use varLabels-names for subsetting - only indexes.
slideSubset
(exprSetArray,i,j): Subsetting; i corresponds to the rows and j corresponds to the slides. j is given by indexes or logicals related to the order of the channel pairs; cf. the constructor slot channels
getIndCy3
(exprSetArray): An accessor function for slot indCy3. The matching pairs of indCy3 and indCy5 define slides.
getIndCy5
(exprSetArray): An accessor function for slot indCy5. The matching pairs of indCy3 and indCy5 define slides.
[
(exprSetArray,i,j,type): A subset operator. Ensures that both exprs and phenoData are subseted properly; but may mix up the pairing of the channels, i.e. the validity of an exprSetArray, if you use type == "invalidExprSetArray"
concatenateExprSetArrays
(objectOne,objectTwo): Concatenates two exprSetArray objects. Genes/rows are assumed to match; identical varLabels are required.
exprSet
(exprSetArray): Class cast, returns an object of exprSet, the channel information is dicarded.

See Also

exprSet-class,exprSet

Examples






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