spikeLI-package

spikeLI


   spikeLI performs a series of analysis of Affymetrix spike-in data
   using inputs from physical-chemistry. It illustrates the advantages
   of such approach in determining expression levels and in identifying
   outliers compared to other methods. The analysis so far is restricted
   to spike-in genes. It will be extended to a generic CEL file.
   spikeLI does not require affy (and it is independent of any other
   bioconductor packages) as it reads spike-in data from a data frame
   variable hgu which is contained in the package.


 package

 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

Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool

spikeLI-package function

spikeLI performs a series of analysis of Affymetrix spike-in data
   using inputs from physical-chemistry. It illustrates the advantages
   of such approach in determining expression levels and in identifying
   outliers compared to other methods. The analysis so far is restricted
   to spike-in genes. It will be extended to a generic CEL file.
   spikeLI does not require affy (and it is independent of any other
   bioconductor packages) as it reads spike-in data from a data frame
   variable hgu which is contained in the package.

spikeLI-package: Analysis of Affymetrix spike-in data (HGU95 and HGU133 Latin square) using the Langmuir Isotherm.

Description

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