Entering edit mode
5.5 years ago
dina.hesham139
▴
170
Hi, I got this error while trying to analyze cuffdiff data with IsoformSwitchAnalyzeR:
> testSwitchList <- importCufflinksFiles(
> + pathToGTF = 'D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/merged.gtf',
> + pathToGeneDEanalysis = 'D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/gene_exp.diff',
> + pathToIsoformDEanalysis = 'D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/isoform_exp.diff',
> + pathToGeneFPKMtracking = 'D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/genes.fpkm_tracking',
> + pathToIsoformFPKMtracking = 'D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/isoforms.fpkm_tracking',
> + pathToIsoformReadGroupTracking = 'D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/isoforms.read_group_tracking',
> + pathToSplicingAnalysis = 'D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/splicing.diff',
> + pathToReadGroups = 'D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/read_groups.info',
> + pathToRunInfo = 'D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/run.info',
> + fixCufflinksAnnotationProblem=TRUE
> + ) Step 1 of 5: Importing data... |================================================================================|100% 78 MB
|================================================================================|100% 111 MB
|================================================================================|100% 32 MB Error in importCufflinksFiles(pathToGTF = "D:/ETMR/ETMR_PNET_NORMAL_cuffdiff/merged.gtf", : The file supplied to pathToGeneDEanalysis does not appear to be the result of the CuffDiff gene expression analysis.
Any help?
Its not anything to do with the fact that you've said your GTF is in the folder
D:/ETMR_PNET_NORMAL_cuffdiff
and all the other files are inD:/ETMR/ETMR_PNET_NORMAL_cuffdiff
is it?Nope, I rewrote the path and still getting the same error.
I will help fixing this problem in the IsoformSwitchAnalyzeR google group forum where it was also posted.
Please do not add an answer unless you're answering the top-level question. This content belongs as a comment and I am moving it to one, but please be more careful in the future.