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="">:

countDaTa

HNmycounts <- HNdata

keepGene=rowSums(edgeR::cpm(HN_mycounts[-1])>0) >=2 #remove genes with count <=1#

table(keepGene)

dim(HN_mycounts)

dim(HN_mycounts[keepGene,])

colData

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))

creating DESeq-dds

dds<-DESeqDataSetFromMatrix(countData=HN_mycounts,colData=metadata,design=~sample,tidy = T)

Updated answer here:

https://support.bioconductor.org/p/122184/