Dear everyone, I tried to create an dds file using codes as follows, however just got a DESeqDataSet unable to be viewed and described as <object with="" null="" pointers="">:
[Codes] HNmycounts <- HNdata keepGene=rowSums(edgeR::cpm(HNmycounts[-1])>0) >=2 sample2<- c(rep("Control",3),rep("Model",3)) sample1<- c("C3", "C5", "C6", "M3", "M7", "M9") metadata<-data.frame(sample1,sample2) names(metadata)<-c("ID","sample") HNmycounts<-HNmycounts[keepGene,] HNmycounts<-HNmycounts[!duplicated(HNmycounts$geneid),] table(duplicated(HNmycounts$geneid)) dds<-DESeqDataSetFromMatrix(countData=HNmycounts,colData=metadata,design=~sample,tidy = T)
countData and colData files are all dataframe format. If anyone could tell where the problem is ? Thanks very much!
