I recently started working with RNA-Seq and I reached the step where I analyze my data using cummeRbund. I thought of doing some tutorials first to get to know the package, but I'm having problems with that.
I followed the instructions in the sample workflow:
cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund"))
But when I run the readCufflinks command, the following errors appear:
Creating database /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/cuffData.db
Reading Run Info File /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/run.info
Writing runInfo Table
Reading Read Group Info /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/read_groups.info
Writing replicates Table
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 thought it was weird, since it is a tutorial data, so the columns should have the correct name? Would this be an issue of installation? Any help is welcomed!