This is a class representation for Probe level Linear
Models fitted to Affymetrix GeneChip probe level data.
probe.coefs
:Object of class "matrix". Contains model
coefficients related to probe effects.
se.probe.coefs
:Object of class "matrix". Contains
standard error estimates for the probe coefficients.
chip.coefs
:Object of class "matrix". Contains model
coefficients related to chip (or chip level) effects for each fit.
se.chip.coefs
:Object of class "matrix". Contains
standard error estimates for the chip coefficients.
const.coefs
:Object of class "matrix". Contains model
coefficients related to intercept effects for each fit.
se.const.coefs
:Object of class "matrix". Contains
standard error estimates for the intercept estimates
model.description
:Object of class "character". This
string describes the probe level model fitted.
weights
:List of objects of class "matrix". Contains probe
weights for each fit. The matrix has columns for chips and rows
are probes.
phenoData
:Object of class "phenoData" This is an
instance of class phenoData
containing the patient
(or case) level data. The columns of the pData slot of this
entity represent variables and the rows represent patients or cases.
annotation
A character string identifying the
annotation that may be used for the ExpressionSet
instance.
experimentData
:Object of class "MIAME". For
compatibility with previous version of this class description can
also be a "character". The class characterOrMIAME
has been
defined just for this.
cdfName
:A character string giving the name of the
cdfFile.
nrow
:Object of class "numeric". Number of rows in chip.
ncol
:Object of class "numeric". Number of cols in
chip.
narrays
:Object of class "numeric". Number of arrays
used in model fit.
normVec
:Object of class "matrix". For storing
normalization vector(s). Not currentl used
varcov
:Object of class "list". A list of
variance/covariance matrices.
residualSE
:Object of class "matrix". Contains residual
standard error and df.
residuals
:List of objects of class "matrix". Contains
residuals from model fit (if stored).
model.call
:Object of class "call"
- weights<-
signature(object = "PLMset")
: replaces the weights.
- weights
signature(object = "PLMset")
: extracts the
model fit weights.
- coefs<-
signature(object = "PLMset")
: replaces the
chip coefs.
- coefs
signature(object = "PLMset")
: extracts the
chip coefs.
- se
signature(object = "PLMset")
: extracts the
standard error estimates of the chip coefs.
- se<-
signature(object = "PLMset")
: replaces the
standard error estimates of the chip coefs.
- coefs.probe
signature(object = "PLMset")
: extracts the
probe coefs.
- se.probe
signature(object = "PLMset")
: extracts the
standard error estimates of the probe coefs.
- coefs.const
signature(object = "PLMset")
: extracts the
intercept coefs.
- se.const
signature(object = "PLMset")
: extracts the
standard error estimates of the intercept coefs.
- getCdfInfo
signature(object = "PLMset")
: retrieve
the environment that defines the location of probes by probe set.
- image
signature(x = "PLMset")
: creates an image
of the robust linear model fit weights for each sample.
- indexProbes
signature(object = "PLMset", which =
"character")
: returns a list with locations of the probes in
each probe set. The list names defines the probe set
names. which
can be "pm", "mm", or "both". If "both" then
perfect match locations are given followed by mismatch locations.
- Mbox
signature(object = "PLMset")
: gives a boxplot of
M's for each chip. The M's are computed relative to a "median"
chip.
- normvec
signature(x = "PLMset")
: will return the normalization vector
(if it has been stored).
- residSE
signature(x = "PLMset")
: will return the residual SE
(if it has been stored).
- boxplot
signature(x = "PLMset")
: Boxplot of Normalized
Unscaled Standard Errors (NUSE).
- NUSE
signature(x = "PLMset")
: Boxplot of Normalized
Unscaled Standard Errors (NUSE) or NUSE values.
- RLE|
signature(x = "PLMset")
: Relative Log Expression
boxplot or values.
This class is better described in the vignette.