Wednesday, October 3, 2012

Problem with loading data into CummeRbund in R

If you have performed RNA-Seq pipeline using Topahat/Bowtie, Cufflinks, Cuffmerge, Cuffdiff and you are trying to load your data into CummeRbund package for R for visualization, you may get the following output:

> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2

> cuff_data <- readCufflinks('diff_out')
Creating database diff_out/cuffData.db
Error in sqliteNewConnection(drv, ...) :
  RS-DBI driver: (could not connect to dbname:
unable to open database file

The problem may seem difficult to solve but actually you haven't set the correct working directory.
to get the working directory,
and the setwd() 
to set the working directory.

You have to set the working directory where your diff_out folder is! But not the diff_out folder itself!

1 comment: