DESeq2 saying that dimensions of count matrix and metadata don't agree, but they do agree

1

Hi all,

I have a counts matrix and a metadata table with the following dimension:

> dim(as.matrix(cts)) 
[1] 6009   60
> dim(colData)
[1] 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 :

Rstudio environment showing cts

Perhaps the rownames are causing issues? I don't know.


expression


R


differential

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