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10-24-2012, 06:17 PM
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#1 |
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Junior Member
Location: Brazil Join Date: Jul 2011
Posts: 6
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CummeRbund error
Hi,
I'm stuck in this cummeRbund error: library(cummeRbund) cuff_data <- readCufflinks('diff_out') Creating database diff_out/cuffData.db Reading diff_out/genes.fpkm_tracking Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 33 elements If someone can help... Thanks |
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11-14-2012, 12:58 PM
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#2 |
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Junior Member
Location: US Join Date: Oct 2012
Posts: 3
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Hi,
I am having the same error: cuff_data <- readCufflinks ('diff_out') Creating database diff_out/cuffData.db Reading diff_out/genes.fpkm_tracking Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 25 elements Were you able to resolve this problem? Thanks. |
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11-14-2012, 01:10 PM
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#3 |
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Junior Member
Location: Brazil Join Date: Jul 2011
Posts: 6
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I look all the files searching the problem...the problem was in the GFF3 (or GTF) file. The '#' character appeared in some gene names.
Probably your annotation file have some character that the R don't recognize. |
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11-14-2012, 04:53 PM
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#4 |
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Junior Member
Location: US Join Date: Oct 2012
Posts: 3
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Thanks. I deleted all the '#' characters and received some progress but another error.
> cuff_data <- readCufflinks ('diff_out') Creating database diff_out/cuffData.db Reading diff_out/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading diff_out/gene_exp.diff Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 14 elements It may just be the same problem but with the gene_exp.diff file this time. Thanks again and I appreciate your help! 
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11-14-2012, 05:14 PM
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#5 |
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Junior Member
Location: Brazil Join Date: Jul 2011
Posts: 6
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I'm glad that I can help.
I ran all the TopHat and cufflinks pipeline with the GFF3 corrected to avoid errors and it worked well for me. |
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12-05-2012, 01:22 PM
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#6 |
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Junior Member
Location: USA Join Date: Oct 2012
Posts: 1
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Hi
I have similar problem while loading database in commeRbund > library("cummeRbund") > cuff_data<-readCufflinks('cuffdiff_output_sample-ATvsBC') Creating database /cuffdiff_output_sample-ATvsBC/cuffData.db Reading Run Info File cuffdiff_output_sample-ATvsBC/run.info Writing runInfo Table Reading Read Group Info cuffdiff_output_sample-ATvsBC/read_groups.info Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 7 elements Then I try > cuff_data CuffSet instance with: 0 samples 0 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS The cuffData.db file is only 70kb, so I assume there are some error in loading db. Any help will be highly appreciated. |
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07-30-2013, 06:37 AM
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#7 | |
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Senior Member
Location: NikoNarita.jp Join Date: Jul 2013
Posts: 142
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Hi there
I got the same problem... any solution ? Quote:
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