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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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Error in `dplyr::full_join()`:! `...` must be empty when creating aSwitchList #197

Open archaemenes opened 1 year ago

archaemenes commented 1 year ago

Please help

cardonaaaa commented 1 year ago

Hi, I'm actually having the same problem. Here I leave my code as example:

switchList <- isoformSwitchAnalysisPart1(switchAnalyzeRlist = switchAnalyzeRlist,
                                         pathToOutput = "outputSequences/",
                                         outputSequences = TRUE,
                                         pathToGTF = "extdata/genome.gtf")

Step 1 of 3 : Detecting isoform switches... Warning: some variables in design formula are characters, converting to factorsStep 2 of 3 : Adding and predicting open reading frames Error in dplyr::full_join(): ! ... must be empty. ✖ Problematic argument: • all = TRUE Backtrace:

  1. IsoformSwitchAnalyzeR::isoformSwitchAnalysisPart1(...)
  2. IsoformSwitchAnalyzeR::addORFfromGTF(...)
  3. IsoformSwitchAnalyzeR::importGTF(...)
  4. dplyr:::full_join.data.frame(...)

Hope we can get any help soon.

archaemenes commented 1 year ago

Updating IsoformSwitchAnalyzeR, dplyr and tidyverse to latest versions as on github worked for me.

cardonaaaa commented 1 year ago

Shouldn't it work with the bioconductor version as well? They highly recommend to download via BiocManager Here is my session info:

other attached packages: [1] dplyr_1.1.2 IsoformSwitchAnalyzeR_1.21.0 ggplot2_3.4.2 DEXSeq_1.46.0
[5] RColorBrewer_1.1-3 AnnotationDbi_1.62.1 DESeq2_1.41.1 SummarizedExperiment_1.30.1 [9] GenomicRanges_1.53.1 GenomeInfoDb_1.37.1 IRanges_2.34.0 S4Vectors_0.38.1
[13] MatrixGenerics_1.13.0 matrixStats_0.63.0 Biobase_2.60.0 BiocGenerics_0.46.0
[17] BiocParallel_1.34.2 limma_3.57.1