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  • godzilla07
    replied
    CummeRbund

    Hi Loyal. I did have write permissions to the directory but I had to use the path to the directory to create cuff_data. I have other problems though which you may help. My RNAseq expt consists of 3 time points which each time point has a control and the experimental condition used. I did a pair wise Cuffdiff for each time point and also created a table of significantly expressed genes for each time point. These are the diff_genes.txt. I don't know how to cluster all of the significant FPKMs of the time points into a single heat map. Also a more simpler question is how to save the plot outputs? I can screen capture the plots but they lose resolution this way. Any suggestions?

    Regards,
    David Kowbel

    Leave a comment:


  • lgoff
    replied
    Originally posted by godzilla07 View Post
    When I try to populate the cuffData.db, I am to be using command lines from the directory that contains the cuffdiff output files. I keep getting this in return.


    > cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund"))
    Creating database /opt/local/lib/R/library/cummeRbund/extdata/cuffData.db
    Error in sqliteNewConnection(drv, ...) :
    RS-DBI driver: (could not connect to dbname:

    I also get the same error message when I use the cuff_data <- readCufflinks('diff_out')

    Could it be that the working directory is not the one that has the cuffdiff output files.
    Please help
    Can you confirm that you have write permissions to this directory?

    -Loyal

    Leave a comment:


  • godzilla07
    started a topic another CummeRbund question

    another CummeRbund question

    When I try to populate the cuffData.db, I am to be using command lines from the directory that contains the cuffdiff output files. I keep getting this in return.


    > cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund"))
    Creating database /opt/local/lib/R/library/cummeRbund/extdata/cuffData.db
    Error in sqliteNewConnection(drv, ...) :
    RS-DBI driver: (could not connect to dbname:

    I also get the same error message when I use the cuff_data <- readCufflinks('diff_out')

    Could it be that the working directory is not the one that has the cuffdiff output files.
    Please help

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