TCGA single dataset normalization

Question

[ruby4bioinfo]

how can i resolve it

 dds <- DESeqDataSetFromMatrix(countData = PAADgenomicMatrix, colData = Samples, design = ~ submitter_id.samples)
Error in DESeqDataSet(se, design = design, ignoreRank) : 
  some values in assay are negative

Answer 1

[ATpoint]

The error is pretty clean. You have a counts table with negative counts. That indicates that these are not raw counts which should be positive integers (or floats depending on the quantification method). DESeq2 requires raw counts. What are these data?