Assesses the efficiency of a two-colour microarray design (D.B. Baird).
Options
PRINT = string tokens |
What to print (design, sed, secontrasts, vcovariance, summary); default desi, sed, seco, vcov, summ |
|---|---|
DYEBIASMETHOD = string token |
Whether to estimate dye bias effects (estimate, omit); default esti |
SPREADSHEET = string tokens |
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.
See also
Procedures: AGBIB, AGLOOP, AGREFERENCE.
Commands for: Microarray data.
Example
CAPTION 'MAEDESIGN example'; STYLE=meta
TEXT TrtLabs; !T('A1B1','A1B2','A2B1','A2B2')
MATRIX [ROWS=!t('A','B','AB'); COLUMNS=TrtLabs;\
VALUES=-1,-1,1,1, -1,1,-1,1, 1,-1,-1,1] Contrasts
CAPTION 'Factorial 2x2 loop design'; STYLE=major
FACTOR [LABELS=TrtLabs; VALUES=1,2,4,3,2,4,3,1,1,2,4,3] Red_Trt1
FACTOR [LABELS=TrtLabs; VALUES=2,4,3,1,1,2,4,3,2,4,3,1] Green_Trt1
MADESIGN [PRINT=design,sed,secontrasts; DYEBIAS=estimate;\
SPREADSHEET=* "sed,secontrasts"] RED=Red_Trt1;\
GREEN=Green_Trt1; XCONTRASTS=Contrasts
CAPTION 'Factorial 2x2 main effect design'; STYLE=major
FACTOR [LABELS=TrtLabs; VALUES=1,3,3,2,4,4,1,1,4,2,2,3] Red_Trt2
FACTOR [LABELS=TrtLabs; VALUES=3,1,1,4,2,2,4,4,1,3,3,2] Green_Trt2
MADESIGN [PRINT=design,sed,secontrasts,vcovariance,summary;\
DYEBIAS=estimate; SPREADSHEET=* "sed,secontrasts"] \
RED=Red_Trt2; GREEN=Green_Trt2; SED=SED_Trts;VCOVARIANCE=VarCov;\
XCONTRASTS=Contrasts; SECONTRASTS=SE_Contrasts