Jim, Thanks for explaining the difference between both. AK On 06-Apr-13 1:47 PM, James W. MacDonald wrote: > Hi Atul, > > On 4/5/2013 7:08 PM, Atul Kakrana wrote: >> Hi Jim, >> >> Thanks. So, I turned the code upside down just to know that it was a >> typo. Your suggestion fixed my problem. >> >> I just have minor doubt: >> >> What is the difference in using >> fit<- lmFit(exprs(esetRMA), design) >> >> OR >> fit<- lmFit(esetRMA, design) >> >> Does this effect result in any possible way? > > No. From ?lmFit: > > |object| > > object of class |numeric|, |matrix|, |MAList|, |EList|, |marrayNorm|, > |ExpressionSet| or |PLMset| containing log-ratios or log-values of > expression for a series of microarrays > > > In the first case you are feeding lmFit a matrix, in the second an > ExpressionSet. Internally lmFit will then do exprs(esetRMA) to get the > data, so the results will be identical. > > Best, > > Jim >> >> Thanks >> >> AK >> >> >> >> >> >> >> On 04/05/2013 06:41 PM, James W. MacDonald wrote: >>> Hi Atul, >>> >>> I think the problem arises because you are using ebayes() instead of >>> eBayes(). See ?eBayes, particularly the part after the Value heading. >>> >>> Best, >>> >>> Jim >>> >>> On 4/5/2013 6:07 PM, Atul Kakrana wrote: >>>> 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 at="" gmail.com="">>>>> <mailto:atulkakrana at="" 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 at r-project.org<mailto:bioconductor at="" r-project.org=""> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >