Error in my DESeq script
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6.4 years ago
sandKings ▴ 40

Could someone please help me troubleshoot this line?

dds <- DESeqDataSetFromMatrix( countData, DataFrame(condition), ~ condition)

I get the error:

Error in if (all(var == var[1])) { : missing value where TRUE/FALSE needed

RNA-Seq R Deseq • 1.4k views
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You probably get NAs somewhere in the building process so var==var[1] is neither TRUE nor FALSE. Do you have NAs in the countData matrix?

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While typing the response to your question, I figured out what I did wrong. The csv file which had my samples and treatments outlined, was for a different cell lineage. I accidentally copied the same file in 2 different folders. So, I didn't have the matching names in the countData. Thanks!!

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It's called rubber-duck debugging. You take a rubber duck, put it next to your screen and explain to it what you did. Most of the time you'll catch the bug. Happy to be a rubber duck. For the next time, try to set up a start to end pipeline without human intervention, these types of errors can have a major effect.

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hahaha! rubber-duck debugging sounds very promising and discreet! Thanks!

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Try removing transcripts with 0 expression value from your dataset.

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