Does analysis of variance for a single-channel microarray design (R.W. Payne & D.B. Baird).
Options
PRINT = string tokens |
Controls printed output (summary, monitoring); default * i.e. none |
|---|---|
TREATMENTSTRUCTURE = formula |
Treatment formula for the analysis; if this is not set, the default is taken from the setting (which must already have been defined) of the TREATMENTSTRUCTURE directive |
BLOCKSTRUCTURE = formula |
Block formula for the analysis; if this is not set, the default is taken from any existing setting specified by the BLOCKSTRUCTURE directive and if neither has been set the design is assumed to be unstratified (i.e. to have a single error term) |
COVARIATE = variates |
Defines any covariates |
FACTORIAL = scalar |
Limit on the number of factors in a treatment term |
SAVETERMS = formula |
Treatment terms for which to save information; if this is not set, information is saved for all the treatment terms |
REPLICATION = pointer |
Pointer to tables saving the replication of the SAVETERMS |
SPREADSHEET = string tokens |
What results to save in spreadsheets (aov, means, vcmeans, effects, vareffects, seeffects, contrasts, secontrasts, tcontrasts, prcontrasts); default * i.e. none |
CONTRASTSLIMIT = scalar |
Limit on the order of a contrast of a treatment term; default 4 |
DEVIATIONSLIMIT = scalar |
Limit on the number of factors in a treatment term for the deviations from its fitted contrasts to be retained in the model; default 9 |
Parameters
Y = variates or pointers |
Y-variates for each analysis |
|---|---|
PROBES = factors or texts |
Defines the probe information for each analysis |
SLIDES = factors or texts |
Defines the slide information for each analysis |
CHECK = texts or variates |
Slide ID’s that can be compared with the labels or levels of the SLIDES factor to ensure that the slide order is correct in each analysis |
IDS = texts |
Saves the probes names that have been generated to label the rows of the output structures from each analysis |
RESIDUALS = matrices |
Saves the residuals |
FITTEDVALUES = matrices |
Saves the fitted values |
MEANS = pointers |
Pointer to a matrix for each of the SAVETERMS, saving the means from each analysis |
VCMEANS = pointers |
Pointer to matrices saving variances and covariances for the means |
EFFECTS = pointers |
Pointer to matrices saving effects |
VAREFFECTS = pointers |
Pointer to variates saving unit variances for effects |
SEEFFECTS = pointers |
Pointer to variates saving effective standard errors of effects |
DF = pointers |
Pointer to variates saving degrees of freedom |
SS = pointers |
Pointer to variates saving sums of squares |
MS = pointers |
Pointer to variates saving mean squares |
RDF = pointers |
Pointer to variates saving degrees of freedom for the residual corresponding to each of the SAVETERMS |
RSS = pointers |
Pointer to variates saving residual sums of squares |
RMS = pointers |
Pointer to variates saving residual mean squares |
VR = pointers |
Pointer to variates saving variance ratios |
PRVR = pointers |
Pointer to variates saving probabilities for the variance ratios |
CONTRASTS = pointers |
Pointer to matrices saving estimates of contrasts |
SECONTRASTS = pointers |
Pointer to matrices saving standard errors of contrasts |
TCONTRASTS = pointers |
Pointer to matrices saving t-statistics for contrasts |
PRCONTRASTS = pointers |
Pointer to matrices saving probabilities for t-statistics of contrasts |
Description
Procedure MAANOVA provides analysis of variance for microarray experiments with single-channel data. The experiment is assumed to consist of several slides, each of which represents a unit of the design. The BLOCKSTRUCTURE and TREATMENTSTRUCTURE options can specify block and treatment formulae (as in ordinary ANOVA) to define the models for the analysis of variance. If the TREATMENTSTRUCTURE option is not set, MAANOVA will use the model already defined by the TREATMENTSTRUCTURE directive, or will fail if that too has not been set. Similarly, if the BLOCKSTRUCTURE option is not set, MAANOVA will use the model (if any) previously defined by the BLOCKSTRUCTURE directive; these can both be omitted if there is only one error term (i.e. if the design is unstratified). The lengths of the block and treatment factors should be the same as the number of slides (and MAANOVA will give a failure diagnostic if this is not so). The FACTORIAL option sets a limit on the number of factors in a treatment term, as in the ANOVA directive. Similarly the CONTRASTSLIMIT and DEVIATIONSLIMIT options operate as the CONTRASTS and DEVIATIONS options of ANOVA.
The COVARIATE option can list any covariates for the analyses; if this is unset, the default is taken from any existing setting defined by the COVARIATE directive. The lengths of the covariates should be the same as the number of slides.
Each slide contains data on a (large) number of probes or genes. MAANOVA does a between-slide analysis of the data on each probe. So, it uses the mean value for any probe observations that are replicated within a slide, and prints a warning if the replication of any probe differs from slide to slide. The data from the slides are specified by the Y, PROBES and SLIDES parameters, and can be in either a stacked or an unstacked representation. With stacked data, the observations from all the slides are supplied by the Y parameter in a single variate. The SLIDES factor indicates the slide on which each observation was made, and the PROBES factor specifies the probe. With unstacked data, the Y parameter supplies a pointer with a variate for each slide, the PROBES factor or text specifies the probes (which must be in the same order on every slide), and the SLIDES factor can be omitted or may be a text defining the labels for each slide. The CHECK parameter can supply a text or variate to be compared with the labels or levels of the SLIDES factor to verify that the slides have been specified in the correct order.
The RESIDUALS and FITTEDVALUES parameters can save the residuals and fitted values, respectively, in a matrix with a row for each probe. The REPLICATION option saves a pointer containing the replication tables for the SAVETERMS. Parameters MEANS and EFFECTS save tables of means and effects from the analysis of each probe. The information is stored in a pointer with a matrix for each of the SAVETERMS. The matrices have a row for each probe, and the columns are labelled to show how they correspond to the cells of the table. (Note that their ordering is the same as the order in which the contents of the REPLICATION table is stored.) Similarly SEEFFECTS saves effective standard errors for the effects, and VCMEANS saves the variances and covariances of the means. VAREFFECTS saves a pointer of variates storing the unit variances of the effects, obtained by the VARIANCE parameter of AKEEP. Parameters DF, SS, MS, RDF, RSS, RMS, VR and PRVR store information from the analysis of variance table, in pointers with a variate for each term and a unit for each probe. DF store the number of degrees of freedom for the relevant term (and probe), SS stores sums of squares, MS stores mean squares, VR stores variance ratios, and PRVR the corresponding probabilities. Similarly the RDF parameter stores the number of degrees of freedom for the appropriate residual for the term, RSS stores the residual sums of squares, and RMS the residual mean square.
Printed output is controlled by the PRINT option, with settings:
monitoring |
to print a running total of the number of probes that have been analysed, and |
|---|---|
summary |
to print a summary of the significance levels found for the probes for each of the SAVETERMS. |
The SPREADSHEET option allows you to save various output components in spreadsheets.
Options: PRINT, TREATMENTSTRUCTURE, BLOCKSTRUCTURE, COVARIATE, FACTORIAL, SAVETERMS, REPLICATION, SPREADSHEET, CONTRASTSLIMIT, DEVIATIONSLIMIT.
Parameters: Y, PROBES, SLIDES, CHECK, IDS, RESIDUALS, FITTEDVALUES, MEANS, VCMEANS, EFFECTS, VAREFFECTS, SEEFFECTS, DF, SS, MS, RDF, RSS, RMS, VR, PRVR, CONTRASTS, SECONTRASTS, TCONTRASTS, PRCONTRASTS.
Method
The analyses are performed by the ANOVA directive.
Action with RESTRICT
If any of the y-variates is restricted, the analysis will involve only the units not excluded by the restriction.
See also
Procedures: AFFYMETRIX, FDRBONFERRONI, FDRMIXTURE, MABGCORRECT, MAEBAYES, MAREGRESSION, MARMA, MAROBUSTMEANS, MAVDIFFERENCE, MAVOLCANO, QNORMALIZE, AYPARALLEL.
Commands for: Microarray data.
Example
CAPTION 'MAANOVA example','Analysis of 9 Arabidopis slides';\
STYLE=meta,plain
ENQUIRE CHANNEL=3(-1); EXIST=check[1...3]; NAME=\
'%GENDIR%/Data/Microarrays/Hyb-Expressions.gsh',\
'%GENDIR%/Data/Microarrays/HybFiles.GSH',\
'%GENDIR%/Data/Microarrays/HybContrasts.GSH'
IF VSUM(check).EQ.3
SPLOAD '%GENDIR%/Data/Microarrays/Hyb-Expressions.gsh'
SPLOAD '%GENDIR%/Data/Microarrays/HybFiles.GSH'
SPLOAD '%GENDIR%/Data/Microarrays/HybContrasts.GSH'
" ANOVA of one-channel microarray data "
TREATMENTSTRUCTURE REG(Target;2;Cont)
BLOCKSTRUCTURE
COVARIATE
MAANOVA [PRINT=summary,monitoring; FACTORIAL=3; ONESHEET=yes;\
"SPREADSHEET=AOV,means,effects,seeffects,teffects,preffects,\
contrasts,secontrasts,tcontrasts,prcontrasts"]\
Y=Expression; SLIDES=Slides; PROBES=Probes; CHECK=FileName;\
IDS=IDProbes; MEANS=Means; EFFECTS=Est; SEEFFECTS=EstSE;\
TEFFECTS=EstT; PREFFECTS=Pr; RMS=RMS; CONTRASTS=ConEst;\
SECONTRASTS=ConSE; TCONTRASTS=ConT; PRCONTRASTS=ConPr
ELSE
CAPTION 'Microarray example datasets have not been installed.'
ENDIF