Estimates expression values from an Affymetrix CED and CDF file (D.B. Baird).
||Method for calculating probe expression values (
||How to transform the data (
||Affymetrix CEL files|
||Associated CDF file|
||Genstat spreadsheet file containing the estimated expression values, together with the associated slide and probe information|
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.
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.
TRANSFORMATION option controls whether the PM and MM values are transformed to logarithms base 2. The default does the transformation only for
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.
Commands for: Microarray data.