I have a counts matrix and a metadata table with the following dimension:
> dim(as.matrix(cts))  6009 60 > dim(colData)  60 4
so that there are 60 samples and 60 corresponding rows of metadata in colData.
The problem that I'm having is the following. Whenever I try to setup the DESeqData object,
# construct DESeqDataSet Object dds <- DESeqDataSetFromMatrix(countData=cts, colData=colData, design=~Condition+Timepoint,tidy=TRUE)
I get the following error:
Error in DESeqDataSetFromMatrix(countData = as.matrix(cts), colData = colData, : ncol(countData) == nrow(colData) is not TRUE
Which doesn't make sense to me. I'm thinking it has something to do with how my cts matrix is setup :
Perhaps the rownames are causing issues? I don't know.