Introduction

A microarray analysis often involves comparing data across different platforms. Unfortunately, significant differences exist among these platforms and data cannot be combined directly.

Probe by probe sequence comparison

This site provides a conversion between different generations of Affymetrix arrays. This is done by masking probes on the raw data(CEL file) that do not meet the requisite conditions. Only probes that have a certain amount of overlap in their nucleotide sequences in both chips are retained for analysis.

How this site works

The user specifies the platforms to be combined and the criteria for selecting the probes. This website then produces a "mask" file. Using the Java application we provide, the user combines this mask file and the original CEL files to generate new CEL files. The new CEL can be processed using the user's favoriate algorithm such as MAS 5.0. Details are available under Instruction.