Class to contain the results of an ilm calculation

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Description

S4 object to contain intensities, probe concentrations, annotations, and summarized expression values.

Slots

Ipm:

A "matrix" of size (number of probes) x (number of CEL-files). Each columns corresponds to one CEL-file with the raw PM.

I0:

A "matrix" of size 1x1 or (number of probes) x (number of CEL-files). In the current release, I0 is set to 0 (default value). In the future releases, I0 will include estimates of background intensities.

probe.concs:

A "matrix" of size (number of probes) x (number of CEL-files) holding the concentration for each probe (picoMolar) computed according to the Langmuir model.

exprSummary:

A "list" with 1 slots, Probe.Set and Cluster.Set, each containing either NA of a matrix of size (number of sets) x (number of CEL-files). Each slot has been included to provide summarized expression values (using medianpolish or transposed medianpolish), computed at the level of Probe Sets (old and new generation arrays), or Cluster Sets (only for whole gene arrays, if probe table contains "Cluster.Set.Name" definition, added manually)

se.exprSummary:

A "list" with 1 slots, Probe.Set and Cluster.Set, each containing either NA of a matrix of size (number of sets) x (number of CEL-files). Each slot has been included to provide standard deviation estimates for summarized expression values, computed for each Probe Set (old and new generation arrays), or Cluster Set (only for whole gene arrays, if probe table contains "Cluster.Set.Name" definition, added manually)

satLim:

Is the "numeric" saturation limit of the intensities of the Langmuir Isotherm, i.e. where the concentration is high or the probe-target binding free energies are large. The default value of A is 10000.

deltaG.pm:

A "matrix" providing the DNA-RNA hybridization free energies (deltaG) computed for each PM probe sequence.

deltaGp.pm:

A "matrix" providing the RNA-RNA hybridization free energies (deltaG) for each PM probe sequence.

info:

A "list" containing several annotations : "ncol" and "nrow" provide the chip dimensions, "cdfName" provides information on the array model,"pmindex" contains the indices of the probes together with the name of the Probe Set, "alpha" is a matrix with intermediate value used by the Langmuir Model (used by the function plotILM), and "probe.table" contains the probe annotation table.

Methods

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Subset ILM objects

getIntens

Get background intensity (of a particular probe set)

getProbeConcs

Get probes concentrations in pM

getExprSummary

Get summarized expression values

getSDSummary

Get estimates for summarized expression values

plotIntens

Plot probe intensities of selected probe set

plotILM

Plot Langmuir Isotherm for selected probe set

Author(s)

Myriam Kroll, Fabrice Berger and Enrico Carlon

Examples

1
showClass("ILM")