
 This selected probe sets information contains the sequence of the selected probe sets, as well as the match and mismatch onformation and Delta G value required for the langmuir analysis


datasets

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

hgu function

A data frame with 11452 observations on the following 9 variables.
  <dl>
    <dt><code>Probe.Set.Name</code></dt><dd>Name of probe set</dd> <dt><code>conc</code></dt><dd>a numeric vector</dd> <dt><code>Ipm</code></dt><dd>a numeric vector</dd> <dt><code>Imm</code></dt><dd>a numeric vector</dd> <dt><code>Seq</code></dt><dd>DNA Sequence of the probe</dd> <dt><code>DGpm</code></dt><dd>DG value of perfect match of the probe</dd> <dt><code>DGmm</code></dt><dd>Delta G value of the mismatch of the probe</dd> <dt><code>DGRNA</code></dt><dd>Delta G value of the RNA</dd> <dt><code>FILE</code></dt><dd>a factor with levels <code>HGU133</code> <code>HGU95</code></dd> </dl> 

Format

This selected probe sets information contains the sequence of the selected probe sets, as well as the match and mismatch onformation and Delta G value required for the langmuir analysis

hgu: Selected Probe Set data

Description

Usage

Arguments

Format

References

See Also

Examples