[BioC] Limma - Result output - Error - Help

[Atul Kakrana]

Hello All,

I wrote a script to analyse affymetrix data but its giving an error
while using the topTable from limma:

Error in array(x, c(length(x), 1L), if (!is.null(names(x)))
list(names(x),  :
  'data' must be of a vector type

I checked all the steps that might be causing the error but couldn't
find out. So, I trimmed my script to minimal basic and it still gives me
same error.

> mydata <- ReadAffy()
> esetRMA <- rma(mydata)
Background correcting
Normalizing
Calculating Expression
> esetRMA
ExpressionSet (storageMode: lockedEnvironment)
assayData: 45101 features, 12 samples
  element names: exprs
protocolData
  sampleNames: 00.0A.CEL 00.0B.CEL ... 12.5C.CEL (12 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: 00.0A.CEL 00.0B.CEL ... 12.5C.CEL (12 total)
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: mouse4302
> sampletype <- c('1','1','1','2','2','2','3','3','3','4','4','4')
> group <-factor(sampletype)
> design<- model.matrix(~0+group)
> colnames(design) <- c('WB','Ten','Eleven','Twelve')
> fit <- lmFit(esetRMA, design)
> contrast.matrix<-makeContrasts(Ten-WB, levels=design)
> fit2<- contrasts.fit(fit,contrast.matrix)
> fit2 <- ebayes(fit2)

> topTable(fit2, adjust = "fdr", number = 50)
Error in 1:ncol(fit) : argument of length 0

> topTable(fit2,coef = 1, adjust = "fdr", number = 50)
Error in array(x, c(length(x), 1L), if (!is.null(names(x)))
list(names(x),  :
  'data' must be of a vector type

> results <- decideTests(fit2)
Error in decideTests(fit2) : Need MArrayLM object


Could anybody please explain me or point out what I am missing here? Its
strange that I wrote a similar script for Illumina which works just fine.

AK

-- 
Atul Kakrana
Delaware Technology Park