oligoPLM-class {oligo} | R Documentation

## Class `"oligoPLM"`

### 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)

[Package oligo version 1.54.1 Index]