aSwitchList <- importRdata( isoformCountMatrix = kallistoQuant$counts, isoformRepExpression = kallistoQuant$abundance, designMatrix = myDesign, isoformExonAnnoation = "/home/lab/project/kallisto_index/hivhuman.gtf", isoformNtFasta = "/home/lab/transcriptome/humantranscript.fa" , showProgress = FALSE ) Step 1 of 6: Checking data... Please note that some condition names were changed due to names not suited for modeling in R. Step 2 of 6: Obtaining annotation... importing GTF (this may take a while) Error in importRdata(isoformCountMatrix = kallistoQuant$counts, isoformRepExpression = kallistoQuant$abundance, : The annotation and quantification (count/abundance matrix and isoform annotation) seems to be different (Jaccard similarity < 0.925). Either isforoms found in the annotation are not quantifed or vise versa. Specifically: 176232 isoforms were quantified. 166883 isoforms are annotated. Only 145874 overlap. 30358 isoforms quantifed isoforms had no corresponding annoation
This combination cannot be analyzed since it will cause discrepencies between quantification and annotation thereby skewing all analysis.
please tell me how i solve this discrepencies. why quantified and annotated values are different. I think is necessary to be same of both value. Thanks
