## Normalisation / Affymetrix gene arrays

### Description

Preprocesses Affymetrix gene array CEL-files to give expression estimates for genes.

### Parameters

Chiptype [empty]

biomaRt annotation [skip]

### Details

Calculates expression estimates using the RMA normalization method and performs log2-transformation. Note that Affymetrix detection calls are not available because there are no mismatch probes.

It is a known problem that a sizeable part of the probes on Affymetrix expression arrays map to wrong genes. In order to circumvent this problem, Chipster uses custom CDF files from the University of Michigan, which remap the probes using current knowledge.

Unfortunately, gene annotations are not directly available for all chip types because of R version inconsistencies and since all custom CDF files are not accompanied with annotation information packages. If needed, these chips can be annotated through the biomaRt service which retrieves gene annotation information from the latest EnsEMBL database online. Please not that EnsEMBL-based annotation are not consistent and vary over time depending from which online database version information is extracted. To use this feature, you also need an internet connection

### Output

A tab-delimited text file containing gene names, gene symbols and expression estimates.