log2 fold change
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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.

deseq2 • 1.1k views
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Entering edit mode
@mikelove
Last seen 8 days ago
United States

Note: I added triple backticks to put the code into a code block (you can also use the "101010" button above the text box)

You can stop at the first error in R, because you will just propagate more errors. The top error says cts doesn't exist.

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