MARMA procedure

Calculates Affymetrix expression values (D.B. Baird).

Options

PRINT = string

What to print (estimates, monitoring); default esti

METHOD = string

Method of establishing grid background (rma, rma2, moments, maximumlikelihood); default rma

NORMALIZED = string

Whether slides have been normalized (yes, no); default no

Parameters

DATA = variates

Perfect-match data

SLIDES = factors

Defines the slides

NEWDATA = variates

Saves the corrected values; if this is unset, they replace the original values in DATA

ESTIMATES = variates

Saves the estimated parameters of the model

Description

MARMA estimates expression values over the pairs of perfect match and mismatches for each probe on Affymetrix slides/chips. On Affymetrix chips, each probe has 8-20 pairs of DNA sequences with a central base changed between the perfect match and mismatch sequences. The value for the probe level of expression is taken as an average over the pairs of perfect-match and mismatch spots.

The default setting of the METHOD option uses the RMA (robust means analysis) probe-level model introduced by Irizarry et al. (2003), which uses only PM information and transforms the values based on a kernel density estimate of the PM distribution. The rma2 setting uses an adaptation of the algorithm which fits the kernel density to a truncated distribution of the perfect-match values, with the truncation point based on an initial kernel density estimate. The moments setting uses the method of moments, and the maximumlikelihood setting uses maximum likelihood.

Options: PRINT, METHOD, NORMALIZED.

Parameters: DATA, SLIDES, NEWDATA, ESTIMATES.

References

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.