TCGA single dataset normalization
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Entering edit mode
27 days ago

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
DESeq2 normalization • 157 views
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Entering edit mode
27 days ago
ATpoint 55k

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?

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