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mmortoglou97
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@mmortoglou97-23827
Last seen 4.7 years ago
I am looking the log2 fold change and when I follow the steps below, these messages are appeared. What am I doing wrong?
dds <- DESeqDataSetFromMatrix(countData = cts,
+ colData = coldata,
+ design= ~ batch + condition)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'ncol': object 'cts' not found
> dds <- DESeq(dds)
Error in is(object, "DESeqDataSet") : object 'dds' not found
> resultsNames(dds) # lists the coefficients
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'mcols': object 'dds' not found
> res <- results(dds, name="condition_trt_vs_untrt")
Error in is(object, "DESeqDataSet") : object 'dds' not found
> res <- lfcShrink(dds, coef="condition_trt_vs_untrt", type="apeglm")
Error in is(dds, "DESeqDataSet") : object 'dds' not found
Thank you in advance.