IvsDG

 Probe set number of the probe set analyzed 

probe_set

conc

outfile


     IvsDG plots intensity vs affinity (or free energy) for a probe
     set at a given concentration. The outcome is compared with the
     prediction from the Langmuir isotherm at that concentration.
     Two graphs are shown: on the left intensity vs. probe number for PM
     (blue) and MM (red); on the right the same value plotted as function
     of the affinities. The black line is the Langmuir Isotherm at the
     given concentration. The two green lines correspond to concentrations
     fourfold higher and lower compared to the given one.


 data

 models

SpikeLI  is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).

Enrico Carlon

spikeLI

Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool

IvsDG function

Probe set number of the probe set analyzed

IvsDG plots intensity vs affinity (or free energy) for a probe
     set at a given concentration. The outcome is compared with the
     prediction from the Langmuir isotherm at that concentration.
     Two graphs are shown: on the left intensity vs. probe number for PM
     (blue) and MM (red); on the right the same value plotted as function
     of the affinities. The black line is the Langmuir Isotherm at the
     given concentration. The two green lines correspond to concentrations
     fourfold higher and lower compared to the given one.

IvsDG: Plot Intensity as function of the affinity for a given probe set at fixed concentration.

Description

Usage

Arguments

References

See Also

Examples