Detection and Restoration of Hybridization Problems in Affymetrix GeneChip Data by Parametric Scanning

Data Supplement

Figures

Fig. 2 Stability in the standards
Fig. 3 Differences from the standard on the cell basis
Fig. 4 Differences from the standard on the window basis
Fig. 5 Effects on the reproducibility of experiments
Fig. 8 Insensitivity to the expectation values

Comparisons with dChip

Cancelled cells/genes and effects on reproducibility in repeated experiments.
to the page

the Software

Instructions
The R function for to start analyses
The R function for Parametric Scanning
The R function for to check the assumptions

Simulation for the sigma

The expectation for the sigma parameter of the median of 25 normalized cells' data
and the R function for reproducing purpose.

26 Oct. 2006, Tomokazu Konishi
Akita Prefectural University

The article is available from the Internet at Genome Informatics Online or SuperNORM.