ilm-methods {affyILM} | R Documentation |
These methods allow to access the results of the function ilm
stored in an object of type ILM
.
getIntens(object,y) getProbeConcs(object,y) getExprSummary(object,y,z) getSDSummary(object,y,z)
object |
An object of type |
y |
A character string or vector of probe set name(s) |
z |
A character string specifying the type of set that is requested |
"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.
A "matrix"
An object of the class ILM
when subsetting "["
Myriam Kroll, Fabrice Berger and Enrico Carlon
## 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"]