MADESIGN procedure

Assesses the efficiency of a two-colour microarray design (D.B. Baird).

Options

PRINT = strings

What to print (design, sed, secontrasts, vcovariance, summary); default desi, sed, seco, vcov, summ

DYEBIASMETHOD = string

Whether to estimate dye bias effects (estimate, omit); default esti

SPREADSHEET = strings

What results to put in spreadsheets (sed, secontrasts, vcovariance); default sed, seco

Parameters

RED = factors

Targets on red dye

GREEN = factors

Targets on green dye

XCONTRASTS = matrices

Contrasts to estimate

SED = symmetric matrices

Saves standard errors of differences

VCOVARIANCE = symmetric matrices

Saves variance and covariances of treatments

SECONTRASTS = symmetric matrices

Saves standard errors of contrasts specified in XCONTRASTS

Description

MADESIGN assesses the efficency of a two-colour microarray design. The RED and GREEN parameters must supply factors defining which treatments are to be allocated to the red and green dyes of each slide, and the XCONTRASTS parameter can supply a matrix defining the contrasts of interest. The DYEBIASMETHOD option indicates whether dyebias is also to be estimated; by default DYEBIASMETHOD=esti.

The SED parameter can supply a symmetric matrix to save the standard errors of differences between treatment means that would arise from the design, assuming a residual mean square of one. The VCOVARIANCE parameter can save a symmetric matrix with variances and covariances of the treatment means, and the SECONTRASTS can save a variate eith the standard errors of the contrasts. The PRINT option controls which of these are printed, and the SPREADSHEET option allows you to put them into GenStat spreadsheets.

Options: PRINT, DYEBIASMETHOD, SPREADSHEET.

Parameters: RED, GREEN, XCONTRASTS, SED, VCOVARIANCE, SECONTRASTS.