Hi Kripa, On 10/11/2012 1:37 PM, Kripa R wrote: > Hi, changing the data to a matrix doesn't help. I think it has > something to do with my design matrix which has NAs > > design <- model.matrix(~0+group, model.frame(~0+group,data, > na.action=NULL)) > > design[55:65,] > group1 group2 > 55 0 1 > 56 1 0 > 57 1 0 > 58 0 1 > 59 1 0 > 60 0 1 > 61 NA NA > 62 1 0 > 63 0 1 > 64 0 1 > 65 1 0 > So right now dim(design): 247 2 and dim(data) 39000 247 > But doing the next two lines results in the same error > data<-as.matrix(data) > fit <- lmFit(data,design) > /Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1)/ > > How could I tell lmFit that when it reaches an NA in the design it > should just ignore the data in the corresponding data column? You don't. If you don't want to fit a model to all of your data, just subset to the data you are interested in and go from there. Best, Jim > > Thanks, > > .kripa > > > Date: Thu, 4 Oct 2012 13:05:33 -0400 > > From: jmacdon at uw.edu > > To: kripa777 at hotmail.com > > CC: bioconductor at r-project.org > > Subject: Re: [BioC] LIMMA: Error in rowMeans(y$exprs, > na.rm=TRUE):'x' must be numeric > > > > Hi Kripa, > > > > On 10/4/2012 12:54 PM, Kripa R wrote: > > > Hi so I'm trying to do limma fitting on my data but i keep getting > the following error > > > Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric > > > But I'm not sure what the problem is does anyone have suggestions? > > > > > > Here's what i've been doing after normalization: > > > data<-subset(data_pheno, select=is.na(data_pheno['case',])==FALSE) > #remove columns with NA > > > group<- factor(data['case',]) > > > design<- model.matrix(~0+group) #dim 240 2 > > > expr<-as.data.frame(data[1:39693,]) #only keep rows that need to > fit aka expression data, dim 39693 240 > > > > > > fit<- lmFit(expr,design) > > > Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric > > > > The help page for lmFit() lists lots of possible input object types, > but > > data.frame is not one of them. Your code is fairly cryptic, so I > have no > > idea what is in that data.frame, other than the obvious conclusion that > > there are some non-numeric data. > > > > You would be better served to use existing infrastructure for > processing > > your data rather than a data.frame. I think there should be enough > > examples in the limma User's Guide to show you the way. > > > > > > Best, > > > > Jim > > > > > > > > > > > > > Thanks, > > > .kripa > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > University of Washington > > Environmental and Occupational Health Sciences > > 4225 Roosevelt Way NE, # 100 > > Seattle WA 98105-6099 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099