Hello All and Abdul,

The fix suggested by Abdul didn't work. I reduced the code to minimal
basic and tried work on other publicly available datasets but the
problem is still the same.


It seems to a bug with Limma or Affy?

Dataset used: http://www.ncbi.nlm.nih.gov/geosuppl/?acc=GSE9711

CODE:
library(affy)
library(limma)

setwd("/home/atul/Dropbox/Analysis/1.iSyTE/test_cel")# Need to change
the directory to where the CEL files are stored
mydata <- ReadAffy()
mydata

esetRMA <- rma(mydata)# RMA from affy was used in iSYTE paper - Ready
made - does Background correction and Normalization by default algos -
See 'affy' manual
esetRMA

sampletype <- c('1','1','1','2','2','2')
design<- model.matrix(~0+factor(sampletype))##  required to avoid intercept
colnames(design) <- c('Cont','Test') ## Personalize the design with col
names

# fit <- lmFit(exprs(esetRMA), design)
fit <- lmFit(exprs(esetRMA), design)
contrast.matrix<-makeContrasts(Test-Cont, levels=design)
fit2<- contrasts.fit(fit,contrast.matrix)
fit2 <- ebayes(fit2)
topTable(fit2, coef = 1, adjust = "BH", 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

I am trying to fix this error from last few days but couldn't find a
solution. I would really appreciate your help.

AK


On 04/05/2013 01:13 AM, abdul rawoof wrote:
> Hello Atul,
>
> Please follow the following script. You need to convert your
> normalised data into expression set value using exprs.
> I hope your problem will solve.
>
> > fit <- lmFit*(exprs(esetRMA)*, design)
> > contrast.matrix<-makeContrasts(Ten-WB, levels=design)
> > fit2<- contrasts.fit(fit,contrast.matrix)
> > fit2 <- ebayes(fit2).
>
>
> On Fri, Apr 5, 2013 at 4:31 AM, Atul Kakrana <atulkakrana@gmail.com
> <mailto:atulkakrana@gmail.com>> wrote:
>
>     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
>
>     _______________________________________________
>     Bioconductor mailing list
>     Bioconductor@r-project.org <mailto:Bioconductor@r-project.org>
>     https://stat.ethz.ch/mailman/listinfo/bioconductor
>     Search the archives:
>     http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>


-- 
Atul Kakrana
Delaware Technology Park


	[[alternative HTML version deleted]]

