Hello! I'm trying to process a SCP dataset, but am getting hung up at the joinAssays step. When using the dataset in this vignette it works as expected: https://bioconductor.org/packages/devel/bioc/vignettes/scp/inst/doc/scp.html. Using the test dataset, I was able to perform the analysis with only the Modified.sequence, Leading.razor.protein, Raw.file, and quantitation columns present, and the "peptides" assay listData contains the Modified.sequence and leading.razor.protein columns. However, when using my own dataset, the "peptides" listData only has the sequence column. I have 144 files but am trying it with just two, and I made sure that there is overlap in the protein accessions (as some digging into the QFeatures documentation told me that if there weren't any proteins in common between the files, it would get dropped from the resulting assay.) My titles are formatted the same as in the test dataset. Any insight?
Hello! I'm trying to process a SCP dataset, but am getting hung up at the joinAssays step. When using the dataset in this vignette it works as expected: https://bioconductor.org/packages/devel/bioc/vignettes/scp/inst/doc/scp.html. Using the test dataset, I was able to perform the analysis with only the Modified.sequence, Leading.razor.protein, Raw.file, and quantitation columns present, and the "peptides" assay listData contains the Modified.sequence and leading.razor.protein columns. However, when using my own dataset, the "peptides" listData only has the sequence column. I have 144 files but am trying it with just two, and I made sure that there is overlap in the protein accessions (as some digging into the QFeatures documentation told me that if there weren't any proteins in common between the files, it would get dropped from the resulting assay.) My titles are formatted the same as in the test dataset. Any insight?