affy (version 1.50.0)

ilm-methods: Methods to access the results of ilm.

Description

These methods allow to access the results of the function ilm stored in an object of type ILM.

Usage

getIntens(object,y)
getProbeConcs(object,y)
getExprSummary(object,y,z)
getSDSummary(object,y,z)

Arguments

object

An object of type ILM

y

A character string or vector of probe set name(s)

z

A character string specifying the type of set that is requested

Value

• A "matrix"

  An object of the class ILM when subsetting "["

Details

"getIntens()" is used to access the intensity values. The probe concentrations are calculated on behalf of the Langmuir model. For each probe (of a probeset) the concentration is estimated in picoMolar and can be accessed via "getProbeConcs()". Medianpolish, Transposed Medianpolish or Median can then be used to compute probeset summarized expression values.

The results can be accessed via "getExprSummary()" and the associated standard deviation is accessed via "getSDSummary()". z, if specified, can take two values : Probe.Set and Cluster.Set (the last one has been created for the definition of cluster sets in the last generation of arrays, whole-gene).

If y=NULL, the results for all probe sets are shown.

See Also

ILM

Examples

## Locate and read in CEL-file
path <- system.file("rawData", "FusionSDK_HG-Focus", "HG-Focus", "2.Calvin",
    package="AffymetrixDataTestFiles")
file1 <- file.path(path,"HG-Focus-1-121502.CEL")
## Calculation of background estimates and expression values (concentrations)
result <- ilm(file1)
## Background intensities of all probes
getIntens(result)
## Background intensities for one or more probesets
getIntens(result,"203561_at") 
getIntens(result,c("203561_at","40359_at"))

## Get concentrations of all probesets
getProbeConcs(result)
## Get concentrations (in picoMolar)
getProbeConcs(result,"203561_at")
getProbeConcs(result,c("203561_at","40359_at"))

## Subsetting
result["203561_at"]