DESEQ2:Error in rownames, what is the problem?

Question

[ciaki]

Hi there,

I am using DESEQ2 for RNAseq analysis but i do not understand why I get this error.

> dds <- DESeqDataSetFromMatrix(countData = data, 
+                               colData = labeldata, 
+                               design =~ subtype, tidy = TRUE)

**Error** in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed

I really do not know what is the issue. Could you please help?

Thanks,

Answer 1

[Kevin Blighe]

Hi,

The error is as stated:

duplicate 'row.names' are not allowed

You should try to find out which rownames are duplicated, and why, via:

rownames(data)[duplicated(rownames(data))]

If you wish to proceed irrespective of this, then change them / make them unique via:

rownames(data) <- make.names(rownames(data))