IsoformSwitchAnalyzeR and cuffdiff data error

Question

[dina.hesham139]

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?

[i.sudbery]

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?

[dina.hesham139]

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

[Kristoffer Vitting-Seerup]

I will help fixing this problem in the IsoformSwitchAnalyzeR google group forum where it was also posted.

[Ram]

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.