Estimates expression values from an Affymetrix CED and CDF file (D.B. Baird).

### Options

`METHOD` = string token |
Method for calculating probe expression values (`mas4` , `mas5` , `rma` , `rma2` ); default `rma` |
---|---|

`TRANSFORMATION` = string |
How to transform the data (`log2` , `none` ); default `none` when `METHOD=mas4` , otherwise `log2` |

### Parameters

`CELFILES` = texts |
Affymetrix CEL files |
---|---|

`CDFFILE` = texts |
Associated CDF file |

`GSHFILE` = texts |
Genstat spreadsheet file containing the estimated expression values, together with the associated slide and probe information |

### Description

`BAFFYMETRIX`

estimates expression values for Affymetrix data. It operates in a “batch” mode, in which each set of CEL files and associated CDF file are loaded into the server, and processed automatically to generate a summary spreadsheet containing the estimates together with the associated slide and probe information.

The `METHOD`

option selects the method to use to summarize over the PM and MM pairs, with settings:

In the Affymetrix MAS 4 and 5 methods, the difference between the signals (PM – MM) is averaged using a robust averaging method. The MAS 4 algorithm uses the AvDiff algorithm which discards the minimum and maximum difference, and any differences greater than 3 standard deviations from the mean. The MAS 5 algorithm uses the Tukey biweight algorithm which reweights the values depending on how far they are from the median, and discards any that are more than 5 times the median absolute distance away. The MAS 5 algorithm also replaces the MM value with a value known as an Ideal Mismatch (IM), which is always less than the PM value.

The `TRANSFORMATION`

option controls whether the PM and MM values are transformed to logarithms base 2. The default does the transformation only for `METHOD`

= `mas5`

, `rma`

or `rma2`

.

Options: `METHOD`

, `TRANSFORMATION`

.

Parameters: `CELFILES`

, `CDFFILE`

, `GSHFILE`

.

### Reference

Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U. & Speed, T.P. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. *Biostatistics*, 4, Number 2, 249-264.

### See also

Procedure: `AFFYMETRIX`

.

Commands for: Microarray data.