Question: Error in running DESeqDataSetFromTximport
gravatar for ankur
13 months ago by
Tezpur University, India
ankur0 wrote:

Hello, I am facing an error while running DESeqDatasetFromTximort after StringTie quantification step

> library(DESeq2)
> sampleTable <- data.frame(condition = factor(rep(c("mock", "mock"), each = 1)))
> rownames(sampleTable) <- colnames(txi$counts)
> dds <- DESeqDataSetFromTximport(txi = txi, sampleTable ,design = ~ Condition + Time)
Error in DESeqDataSet(se, design = design, ignoreRank) : 
  all variables in design formula must be columns in colData

My sample contains:

Sample_ids Condition Time

t_data_9.ctab Mock 6hpi

t_data_10.ctab Mock 6hpi

Am, I supposed to add any argument?

ADD COMMENTlink modified 13 months ago by Devon Ryan93k • written 13 months ago by ankur0
gravatar for Devon Ryan
13 months ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

You need to redo how sampleTable is made. Firstly, it needs to have Condition rather than condition (or you need to change that in your design) and secondly it needs to contain Time, which it currently doesn't. Fixing that will remove the error.

ADD COMMENTlink written 13 months ago by Devon Ryan93k
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