DeSEQ 2 Error: some values in assay are negative
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@6d47e22d
Last seen 8 months ago
Pakistan

Hi! Am a complete beginner to using DESeq2. I have read the vignette and am encountering an error when I am trying to create a DESeqDataSet from the count data. I am getting an error that some of the values in the assay are negative. However, I have scanned the data set and there are no negative integers. Also i removed the genes with zero values from my data set and started again but still getting the same error. Would be grateful if some one can help me here.

Code should be placed in three backticks as shown below

``dds <-DESeqDataSetFromMatrix(countData=countData,colData=colData, design= genotype+BDQ_treatment)enter code here

Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative

sessionInfo( )

```

Countmatrix negativeassay DESeq2 • 1.5k views
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Entering edit mode

In order to back up your assertion that there are no negative values, you should provide evidence. For example

any(countData < 0)
dds <- DESeqDataSetFromMatrix(countData=countData,colData=colData, design= genotype+BDQ_treatment)

The first test is what is giving the error, and I would be quite surprised if it returns FALSE on a direct test and then TRUE once placed within a SummarizedExperiment.

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@mikelove
Last seen 16 hours ago
United States

You don't need to remove 0's.

What do you get with

any(countData < 0)

(fixed, typo first time around)

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Thank you for your help.

We checked our columns and rows from the count data and col file and we were missing one sample. Also there was a "-" instead of a _ in one of the IDs in the col data.

We ve been able to create our DESeqDataMatrix after correcting for these errors.

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