Instructions

1. Obtain the AffyBatch form of data

Put the cel. files you wish to analyze into the current directory of the R,
copy this page and paste it to the R console.

2. Remove the failures

Copy this page and paste it to the console.
The R will ask you the value for the expectation parameter.
My suggestion for the parameter to start with is 2.

The affected cells will be removed from the input, Adata.
Affected cells are indicated by NAs in a file named "flag".
Pseudo image and positions of the failure cells will be produced.

3. Check the requested conditions by means of your subjects

To get the QQ plots and the histogram for the sd value,
Copy this page and paste it to the console.

Miscellaneous

Introduction to the R and the program packages required

Check the homepage for the R program.
The packages required are available at BioC install page.

An alternative choice for analyses

Outsourcing service for normalizing GeneChip data
is available through Skylight Biotech Inc.,
and the service includes the parametric scanning as a default.
The normalized data will be supplied in csv format,
which can be read by MS-Excel and/or GeneSpring.

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