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  • #16
    i've got the same problem, just can not readcufflinks() correctly, and i wonder whether u solve the issue or not?

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    • #17
      Sorry,I haven't already solved the problems in cummeRbund packages. If there is any other way can address, please reply for me.
      Thanks a lot.

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      • #18
        Same issue: can't create the database using readCufflinks

        HTML Code:
        > cuff_data <- readCufflinks("diff_out_R", rebuild = TRUE)
        Creating database diff_out_R/cuffData.db
        Reading Run Info File diff_out_R/run.info
        Writing runInfo Table
        Reading Read Group Info  diff_out_R/read_groups.info
        Writing replicates Table
        Reading Var Model Info  diff_out_R/var_model.info
        Writing varModel Table
        Reading diff_out_R/genes.fpkm_tracking
        Checking samples table...
        Populating samples table...
        Error: Column name mismatch.
        In addition: There were 50 or more warnings (use warnings() to see the first 50)
        I think this is something to do with the updated version, since it worked when I used the same files with a previous version, but with this version they don't work anymore.

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        • #19
          Does anyone have a good solution for these errors? Mine looks like this:

          Creating database /cuffData.db
          Error in rsqlite_connect(dbname, loadable.extensions, flags, vfs) :
          Could not connect to database:
          unable to open database file

          or

          50+ of these:

          1: In rsqlite_fetch(res@ptr, n = n) :
          Don't need to call dbFetch() for statements, only for queries

          depending on how I submit it

          From what I've read people have solved these issues by altering with the input (no symbols in the table) or by correcting the working directory. I have tried these and everything else I can think of. I have tried a cuffdiff output from a previous version and experiment and it runs in cummerbund fine...

          I'm stuck. does anyone have a suggestion?

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          • #20
            Hi jkofsky -

            We are just having the same discussion in biocinductor - and we came across with some alternatives since seems to be a bug in the new version of bioconductor/cummeRbund. Here you are the link.



            Hope it helps.

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            • #21
              Originally posted by Oskar View Post
              Hi jkofsky -

              We are just having the same discussion in biocinductor - and we came across with some alternatives since seems to be a bug in the new version of bioconductor/cummeRbund. Here you are the link.



              Hope it helps.
              Thanks, I will follow the thread.

              I'm a little hesitant to assume its a bug considering data from cuffdiff (that was produced a year ago) is working fine ....

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