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IsoformSwitchAnalyzeR and cuffdiff data error

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?

rna-seq isoformswitchanalyzer
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updated by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup • written by dina.hesham139 dina.hesham139

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 in D:/ETMR/ETMR_PNET_NORMAL_cuffdiff is it?

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written by i.sudbery i.sudbery

Nope, I rewrote the path and still getting the same error.

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written by dina.hesham139 dina.hesham139

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.

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written by Ram Ram

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