I have run cuffDiff on my data. The out put of the cuffdiff is in a directory named "tx_win_cuffdiff_output". I am trying to analyse it in cummeRbund. The system and R information is as follows:
> platform x86_64-w64-mingw32 arch x86_64 os mingw32 system x86_64, mingw32 status major 3 minor 4.2 year 2017 month 09 day 28 svn rev 73368 language R version.string R version 3.4.2 (2017-09-28) nickname Short Summer
I ran the following command after loading cummeRbund library
> (cummeRbund) cuff <- readCufflinks(dbFile = "cuffData.db", dir="tx_win_cuffdiff_output", gtfFile = "tx_win_cuffdiff_output/transcripts.gtf", genome = "tx_win_cuffdiff_output/SuperDuper.fasta.fasta",rebuild =T)
Following error is shown:
Creating database tx_win_cuffdiff_output/cuffData.db Reading Run Info File tx_win_cuffdiff_output/run.info Writing runInfo Table Reading Read Group Info tx_win_cuffdiff_output/read_groups.info Writing replicates Table Reading Var Model Info tx_win_cuffdiff_output/var_model.info Writing varModel Table Reading GTF file Writing GTF features to 'features' table... Reading tx_win_cuffdiff_output/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)
Where did I erred.