[BioC] error in maanova matest() with affymetrix

[James W. MacDonald]

Hi Georg,

Georg Otto wrote:
> Hi,
> 
> some time ago i tried to use maanova to analyse a microarray
> experiment using affymetrix chips. This did not work, since the
> function matest gave an error. At that time, my question to the
> mailing list could not be solved. Now, some versions of maaonova and R
> later, I tried again, resulting in the same error. Maybe this time,
> somebody could give me a hint how to solve this or share some methods
> how to analyse affymetrix experiments using maanova.

You could always look at the last section of the maanova vignette, which 
shows exactly how to analyze affy experiments using maanova (and _does_ 
mention that you cannot fit a dye or array effect, which likely is the 
cause of your problem).

Best,

Jim


> 
> Here is my code:
> 
> ## Generate ExpressionSet object and import data 
>> library(affy)
>> library(maanova)
> 
>> cel.path<-"../stages/quantification"
>> targets<-new("AnnotatedDataFrame")
>> pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2)
> 
>> Data<-ReadAffy(celfile.path =cel.path,
>   +             filenames = sampleNames(targets),
>   +             verbose=TRUE)
>> eset<-rma(Data)
> 
>> write.exprs(eset, file="expression.txt")
>> design.matrix<-data.frame(Array=row.names(pData(targets)),
>   +                        Stage=pData(targets)$Stage,
>   +                        Sample=c(1:length(row.names(pData(targets)))),
>   +                        Dye=rep(1, times=length(row.names(pData(targets)))))
> 
>> write.table(design.matrix, "design.txt", sep="\t", row=FALSE, quote=FALSE)
>> data.raw<-read.madata("expression.txt", designfile="design.txt", cloneid=1, pmt=2, spotflag=FALSE)
> 
> ## this gives a warning
> Warning messages:
> 1: No meta row information, use 1 instead! in: read.madata("expression.txt", designfile = "design.txt", cloneid = 1,  
> 2: No meta column information, use 1 instead! in: read.madata("expression.txt", designfile = "design.txt", cloneid = 1,  
> 3: No row information. in: read.madata("expression.txt", designfile = "design.txt", cloneid = 1,  
> 4: No column information. in: read.madata("expression.txt", designfile = "design.txt", cloneid = 1,  
> 
> ## import data and perform F-test
>> data.maanova<-createData(data.raw, n.rep=1, log.trans=F)
>> model.full.mix<-makeModel(data=data.maanova,
>   +      formula=~Array+Sample+Stage, random=~Array+Sample)
>> anova.full.mix<-fitmaanova(data.maanova, model.full.mix)
>> test.Stage.mix<-matest(data.maanova, model.full.mix, term="Stage", n.perm=100)
> 
> ## This gives the following error:
> 
> Doing F-test on observed data ...
> Error in var(log(Chis)) : missing observations in cov/cor
> In addition: Warning message:
> NAs produced in: rchisq(n, df) 
> 
>> traceback()
>  
> 4: var(log(Chis))
> 3: meanvarlog(df.random)
> 2: matest.engine(anovaobj, term, test.method = test.method, Contrast = Contrast, 
>        is.ftest = is.ftest, verbose = FALSE)
> 1: matest(data.maanova, model.full.mix, term = "Stage", n.perm = 100)
> 
>> sessionInfo()
> 
> R version 2.5.0 (2007-04-23) 
> x86_64-redhat-linux-gnu 
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets" 
> [7] "methods"   "base"     
> 
> other attached packages:
> zebrafishcdf      maanova         affy       affyio      Biobase 
>     "1.16.0"      "1.6.0"     "1.14.0"      "1.4.0"     "1.14.0" 
> 
> 
> Cheers,
> 
> Georg
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623