Hi, I 'm trying to analyze my kallisto data with IsoformSwitchAnalyzeR but I get this error when I use the importRdata function, I get this error:
> aSwitchList <- importRdata( + isoformCountMatrix = mySwitchList$counts, + isoformRepExpression = mySwitchList$abundance, + designMatrix = designMatrix, + isoformExonAnnoation = "/rice/Oryza_sativa.IRGSP-1.0.37.gtf", + showProgress = T) Step 1 of 6: Checking data... Step 2 of 6: Obtaining annotation... importing GTF (this may take a while) converting annotated CDSs Error in importRdata(isoformCountMatrix = mySwitchList$counts, isoformRepExpression = mySwitchList$abundance, : The annotation and quantification (count/abundance matrix and isoform annotation) seems to be different (jacard similarity < 0.95). Either isforoms found in the annotation are not quantifed or vise versa. Specifically: 42346 isoforms were quantified. 98663 isoforms are annotated. Only 42346 overlap. This combination cannot be analyzed since it will cause discrepencies between quantification and annotation thereby skewing all analysis. Please make sure they belong together and try again. For more info see the FAQ in the vignette.