Normalization of Various Array Types

BIOS 691-803; Spring 2010
Instructor: Dr. Mark Reimers, VCU


Expression Summarization
Intro to other array assays
CGH array analysis
ChIP-chip analysis
Methylation chip analysis
SNP chip analysis

Web Resources

StepGram homepage
Wikipedia ChIP-chip



The factor method for summarization. [PRESENTABLE]
Jean Wu's paper on gcRMA. [PRESENTABLE]
Here is a review article describing CGH on arrays.
Sven Bilke did a nice treatment of biases in CGH probes here.
Adam Olshen did the first serious statistical treatment of CGH data using Maximum Likelihood methods here.
Doron Lipson wrote a very efficient method (StepGram) described in his Interval Mapping(StepGram) paper, and his Poster


Here's a biologically oriented intro to ChIP-chip assays.
Shirley Liu's lab produced a better method for normalizing Affy ChIP arrays.
Wing Wong's lab produced an improvement on the moving average method here.

Methylation arrays

Rafa Irizarry's paper compares several methods for measuring and analyzing methylation data.

SNP chip

About SNP arrays
The CRLMM paper