another CummeRbund question

[godzilla07]

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

[lgoff]

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

[godzilla07]

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