I've got RNAseq data which was processed and given to me in a text-file. The rows are EnsemblIDs, and the columns the individuals with their counts.
I've loaded these data, and ran DESeq2. Now I want to plot the log2 fold changes similar as is explained here: http://www.bioconductor.org/help/workflows/rnaseqGene/#plotting-fold-changes-in-genomic-space. Thing is, I need to 'manually' plug in the "GRanges" in the SummarizedExperiment object.
I could use some pointers - I have no idea how to start. Below the command I've used and the error message.
resGR <- results(RAW_DESeq2AF, lfcThreshold = 1, format = "GRanges")
>Error in results(RAW_DESeq2AF, lfcThreshold = 1, format = "GRanges") : >rowRanges is GRangesList and one or more GRanges have length 0. Use format='DataFrame' or 'GRangesList'