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Code should be placed in three backticks as shown below

> dds <- DESeqDataSetFromMatrix(countData = cts,
+                               colData = coldata,
+                               design = ~ condition)
Error in DESeqDataSet(se, design = design, ignoreRank) : 
  NA values are not allowed in the count matrix

> any(is.na(cts))
[1] TRUE
> all(is.numeric(cts))
[1] TRUE


Hello, 
I don't have any missing values in my data, but I keep getting such message. 
Dose anybody know the solution? Thanks

You have NAs in your matrix, simple as that. The check that runs internally is really just a any(is.na(cts)). Your check is.numeric() is not informative, as NAs in a numeric matrix are also numeric.

This is TRUE: is.numeric(matrix(c(1,NA)))

You can see the rows in which there are NAs with something like:

# The second row has NAs
cts <- matrix(c(1,4,3,5,6,3,NA,8), 2, byrow=TRUE)
rowsWithNAs <- which(rowSums(is.na(cts))>0)
cts[rowsWithNAs,]