Difference between revisions of "Affymetrix normalization (analysis)"

Revision as of 16:27, 4 April 2013

Affymetrix Normalization

Normalization of Affymetrix CEL files based on the functions of the Bioconductor AFFY package.

Parameters:

• CEL file - the path to the CEL file.
• Method (normalize AFFY function) - A generic function which normalizes microarray data. Normalization is intended to remove from the intensity measures any systematic trends which arise from the microarray technology rather than from differences between the probes or between the target RNA samples hybridized to the arrays.
• Background Correction (bgcorrect.method) - the name of the background adjustment method.
• Normalization method (normalize.method) - the normalization method to use.
• PM correction (pmcorrect.method) - the name of the PM adjustment method.
• Summarization (summary.method) - the method used for the computation of expression values.
• CDF version - version of Affymetrix CDF file.
• Output name - the name of the output data file.

Original names of the AFFY functions used for analysis are shown in parentheses. For a detailed description of these functions see the AFFY reference manual.

Note: Before the CEL normalization is started you need to install R and Rserve on your computer. For more information on installing, please visit R-project website.