ScientificProblem: AffyMicroarrayExperiment

ScientificGoal:

The user wishes to identify genes whose expression is significantly altered in a 'sample' compared to a 'control'

ProblemDescription:

A user has performed a microarray experiment using the Affymetrix system for studing global gene expression.

In the simplest case a number of replicate control data are compared to a number of replicate data derived from 'treated' or 'disease' samples.

The end result of the experiment is essentially:

• A file that contains intensity and standard deviation data for each probe feature on the chip.

• A file that contains information on the array type and some experimental details.

• A large, raw image file produced directly from the array scanner.

• A file (*.chp) that contains data extracted from the image file. This file can contain both absolute analysis and comparison data that describes a number of attributes of the experiment and the signals for each 'gene' represented on the chip. This is the most useful data source for identifying genes with modified expression.

The *.chp file is usually loaded into a data analysis package or spreadsheet to perform further analysis.

PrimaryActor:

A biologist

An Affymetrix Microarray Analysis Service

DataSets:

See the four datasets outlined above.

CurrentSolution:

A number of solutions are currently available. Affymetrix provide software for basic analysis, called the data mining tool. There are many other data analysis packages available that can handle Affy data including open source project such as Bioconductor for the 'R' statistical analysis package.

MyGridSolution:

The MyGrid solution ideally will provide a series of analysis steps for data derived from the .chp files, including thresholding and normalisation. The data should be made available in a form amenable to simple querying. The end result will be the identification of a number of 'interesting' genes derived according to user specified parameters.

Links to UserInterviews, FreeTextCases, LiteratureCases and ScientificProblems:

Notes:

More information about Affy gene chips:

HGMP

Affymetrix Homepage

-- AnilWipat - 05 Jan 2003