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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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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.Comment
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Same issue: can't create the database using readCufflinks
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.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)Comment
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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?Comment
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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.Comment
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Thanks, I will follow the thread.Originally posted by Oskar View PostHi 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.
I'm a little hesitant to assume its a bug considering data from cuffdiff (that was produced a year ago) is working fine ....Comment
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