oligoPLM-class: Class '"oligoPLM"'

In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays

Description

A class to represent Probe Level Models.

Objects from the Class

Objects can be created by calls of the form fitProbeLevelModel(FeatureSetObject), where FeatureSetObject is an object obtained through read.celfiles or read.xysfiles, representing intensities observed for different probes (which are grouped in probesets or meta-probesets) across distinct samples.

Slots

chip.coefs:

"matrix" with chip/sample effects - probeset-level

description:

"MIAME" compliant description information.

phenoData:

"AnnotatedDataFrame" with phenotypic data.

protocolData:

"AnnotatedDataFrame" with protocol data.

probe.coefs:

"numeric" vector with probe effects

weights:

"matrix" with weights - probe-level

residuals:

"matrix" with residuals - probe-level

se.chip.coefs:

"matrix" with standard errors for chip/sample coefficients

se.probe.coefs:

"numeric" vector with standard errors for probe effects

residualSE:

scale - residual standard error

geometry:

array geometry used for plots

method:

"character" string describing method used for PLM

manufacturer:

"character" string with manufacturer name

annotation:

"character" string with the name of the annotation package

narrays:

"integer" describing the number of arrays

nprobes:

"integer" describing the number of probes before summarization

nprobesets:

"integer" describing the number of probesets after summarization

Methods

annotation

signature(object = "oligoPLM"): accessor/replacement method to annotation slot

boxplot

signature(x = "oligoPLM"): boxplot method

coef

signature(object = "oligoPLM"): accessor/replacement method to coef slot

coefs.probe

signature(object = "oligoPLM"): accessor/replacement method to coefs.probe slot

geometry

signature(object = "oligoPLM"): accessor/replacement method to geometry slot

image

signature(x = "oligoPLM"): image method

manufacturer

signature(object = "oligoPLM"): accessor/replacement method to manufacturer slot

method

signature(object = "oligoPLM"): accessor/replacement method to method slot

ncol

signature(x = "oligoPLM"): accessor/replacement method to ncol slot

nprobes

signature(object = "oligoPLM"): accessor/replacement method to nprobes slot

nprobesets

signature(object = "oligoPLM"): accessor/replacement method to nprobesets slot

residuals

signature(object = "oligoPLM"): accessor/replacement method to residuals slot

residualSE

signature(object = "oligoPLM"): accessor/replacement method to residualSE slot

se

signature(object = "oligoPLM"): accessor/replacement method to se slot

se.probe

signature(object = "oligoPLM"): accessor/replacement method to se.probe slot

show

signature(object = "oligoPLM"): show method

weights

signature(object = "oligoPLM"): accessor/replacement method to weights slot

NUSE

signature(x = "oligoPLM") : Boxplot of Normalized Unscaled Standard Errors (NUSE) or NUSE values.

RLE

signature(x = "oligoPLM") : Relative Log Expression boxplot or values.

opset2eset

signature(x = "oligoPLM") : Convert to ExpressionSet.

Author(s)

This is a port from Ben Bolstad's work implemented in the affyPLM package. Problems with the implementation in oligo should be reported to the package's maintainer.

References

Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. PhD Dissertation. University of California, Berkeley.

See Also

rma, summarize

Examples

## TODO: review code and fix broken
## Not run: 
if (require(oligoData)){
  data(nimbleExpressionFS)
  fit <- fitProbeLevelModel(nimbleExpressionFS)
  image(fit)
  NUSE(fit)
  RLE(fit)
}

## End(Not run)

jmacdon/oligo documentation built on Aug. 11, 2020, 12:32 a.m.