Estimates treatment effects from a two-colour microarray design (D.B. Baird).
Options
PRINT = string tokens |
What to print (design, summary, monitoring); default desi, summ, moni |
|---|---|
DYEBIASMETHOD = string token |
Whether to estimate dye bias effects (estimate, omit); default esti |
SPREADSHEET = string tokens |
What results to put in spreadsheets (estimates, df, rsd, dyebias, seestimates, tvalues, probabilities, contrasts, secontrasts, tcontrasts, prcontrasts); default esti, df, rsd, dyeb, sees, tval, prob, cont, seco, tcon, prco |
Parameters
LOGRATIOS = variates or pointers |
Log-ratios |
|---|---|
PROBES = factors or texts |
Probes for the log-ratios |
SLIDES = factors or texts |
Slides for the log-ratios |
REDTREATMENTS = factors |
Targets on red dye for slides |
GREENTREATMENTS = factors |
Targets on green dye for slides |
CHECK = texts or variates |
Slide ID’s of the red and green treatments for a check matching the slide order with the labels or levels of SLIDE |
XCONTRASTS = matrices |
Contrasts to estimate |
IDPROBES = texts |
Saves the probe names for each output row |
DF = variates |
Saves degrees of freedom for t-values |
RSD = variates |
Saves the residual standard deviation |
DYEBIAS = variates |
Saves estimated dye swap bias effects |
ESTIMATES = pointers |
Saves the estimates |
SEESTIMATES = pointers |
Saves the standard errors of the estimates |
TVALUES = pointers |
Saves t-values of the estimates |
PROBABILITIES = pointers |
Saves probabilities for the t-values |
CONTRASTS = pointers |
Saves estimates of the contrasts |
SECONTRASTS = pointers |
Saves the standard errors of the contrasts |
TCONTRASTS = pointers |
Saves t-values for the contrasts |
PRCONTRASTS = pointers |
Saves probabilities for the contrasts |
Description
MAESTIMATE estimate effects from the within-slide differences between targets (or treatments). This information is contained in the log-ratios. Usually, these log-ratios will have normalized using the MNORMALIZE procedure. MAESTIMATE uses analysis of variance with a pooled error across the targets (i.e. treatments) for each probe (or gene). The normalization of each slide effectively removes the block effects, so the log-ratios now reflect the differences between treatments on each slide, and the constant represents the dye-swap effect for the probe. The DYEBIASMETHOD option controls whether or not the dye biases are estimated, and the XCONTRASTS parameter allows you to specify a matrix defining contrasts to estimate between treatments.
The log-ratios are supplied by the DATA parameter. If these are in a single variate, the SLIDE parameter should supply a factor to index the slides, and the PROBES parameter should index the probes or genes. Alternatively, you can supply a pointer containing a variate for each slide. The SLIDES parameter can then be omitted, or it can supply a text with an entry for each slide. The PROBES parameter can supply either a factor or a text, defining the probes on a single slide, and all slides must have a common layout.
The REDTREATMENTS parameter should supply a factor to indicate the target assigned to the red dye. This is assumed to be the channel on the top of the log-ratios. This factor must have the same number of values as the number of levels of the Slides factor. Similarly, the GREENTREATMENTS parameter should supply a factor to indicate the target assigned to the green dye. The CHECK parameter can supply a text or variate identifying the slide in each unit of the REDTREATMENTS and GREENTREATMENTS factors. This can then be used to check that these units match the slides according to the labels or levels of the SLIDE factor. If the labels of the slides and check factor match, but are in a different order, the treatment factors will be sorted into the correct order, and a warning is given.
The other parameters allow you to save results from the analysis, and the SPREADSHEET option allows these to be put into Genstat spreadsheets.
Options: PRINT, DYEBIASMETHOD, SPREADSHEET.
Parameters: LOGRATIOS, PROBES, SLIDES, REDTREATMENTS, GREENTREATMENTS, CHECK, XCONTRASTS, IDPROBES, DF, RSD, DYEBIAS, ESTIMATES, SEESTIMATES, TVALUES, PROBABILITIES, CONTRASTS, SECONTRASTS, TCONTRASTS, PRCONTRASTS.
See also
Procedures: DMADENSITY, FDRBONFERRONI, FDRMIXTURE, MACALCULATE, MAHISTOGRAM, MAPCLUSTER, MAPLOT, MASCLUSTER, MASHADE, MAVOLCANO, MA2CLUSTER, MNORMALIZE.
Commands for: Microarray data.
Example
CAPTION 'MAESTIMATE example'; STYLE=meta
ENQUIRE CHANNEL=3(-1); EXIST=check[1...3]; NAME=\
'%GENDIR%/Data/Microarrays/ApoAIKnockOutStacked.GSH',\
'%GENDIR%/Data/Microarrays/ApoAIKnockOutSlides.gsh',\
'%GENDIR%/Data/Microarrays/ApoAIKnockOutContrast.GSH'
IF VSUM(check).EQ.3
SPLOAD '%GENDIR%/Data/Microarrays/ApoAIKnockOutStacked.GSH'
SPLOAD '%GENDIR%/Data/Microarrays/ApoAIKnockOutSlides.gsh'
SPLOAD '%GENDIR%/Data/Microarrays/ApoAIKnockOutContrast.GSH'
" Estimate Effects from Microarray Data."
MAESTIMATE [PRINT=design,summary; DYEBIAS=omit;\
SPREADSHEET=* "df,rsd,estimates,seestimates,tvalues,\
probabilities,contrasts,secontrasts,tcontrasts,prcontrasts"]\
LOGRATIO=cLogRatio;SLIDES=Slide; PROBES=NAME;\
REDTREATMENTS=Red_Treat; GREENTREATMENTS=Green_Treat;\
CHECK=SlideName; XCONTRASTS=KOvsN; IDPROBES=Probes; DF=DF;\
RSD=Res_SD; ESTIMATES=Est; SEESTIMATES=SE; TVALUES=TEst;\
PROBABILITIES=PrEst; CONTRASTS=Cont; SECONTRASTS=SECont;\
PRCONTRASTS=PrCon; TCONTRASTS=TCon
ELSE
CAPTION 'Microarray example datasets have not been installed.'
ENDIF