exprSetArray-class {arrayMagic} | R Documentation |
This is class representation for cDNA Microarray Data
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
)
indCy3
:indCy5
:exprs
:channels
define
slides and rows representing genes. se.exprs
:exprs
which contains
standard error estimates for the estimated expression levels. phenoData
:phenoData
containing channel annotations. The columns of the
pData slot of this entity represent
variables and the rows represent channels. notes
: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.
getExprSetDiff
exprSet
object of the expression levels of channel Cy3exprSet
object of the expression levels of channel Cy5phenoData
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.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.phenoData
object of the annotation information given for channel Cy3.
Do not use varLabels-names for subsetting - only indexes.pData
object given by phenoDataCy3
.
Do not use varLabels-names for subsetting - only indexes.phenoData
object of the annotation information given for channel Cy5.
Do not use varLabels-names for subsetting - only indexes.pData
object given by phenoDataCy5
.
Do not use varLabels-names for subsetting - only indexes.channels
indCy3
. The matching pairs of indCy3 and indCy5 define slides.indCy5
. The matching pairs of indCy3 and indCy5 define slides.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"exprSetArray
objects. Genes/rows are assumed to match;
identical varLabels
are required.exprSet
, the channel information is dicarded.
exprSet-class,exprSet