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Old 10-17-2013, 12:37 PM   #1
Palgrave
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Location: norway

Join Date: Aug 2011
Posts: 73
Default [solved]cummeRbund error message

Running cummeRbund gives me the following error:

> cuff_data <- readCufflinks("~/cufflinks/control")
> csDensity(genes(cuff_data))
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)


Anyone know why? It workes with a different sample.

Last edited by Palgrave; 10-17-2013 at 12:42 PM.
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Old 10-17-2013, 12:41 PM   #2
Palgrave
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Solved by removing cuffData.db from directory.
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Old 10-18-2013, 12:26 AM   #3
IBseq
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Dear all,
any suggestion about this issue I have?

I run the following commands:
> library (cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
> cuff<-readCufflinks ()
> cuff
CuffSet instance with:
2 samples
24302 genes
42262 isoforms
28828 TSS
25037 CDS
24302 promoters
28828 splicing
0 relCDS
> iso.diff <- diffData(isoforms(cuff))
> iso.diff.top <- iso.diff[order(iso.diff$q_value),][1:20,]
> iso.diff.top
isoform_id sample_1 sample_2 status value_1 value_2
19598 TCONS_00019647 q1 q2 OK 0.00142518 63.8030
23003 TCONS_00023056 q1 q2 OK 0.01873000 267.5380
16085 TCONS_00016126 q1 q2 OK 0.00828880 53.7744
20375 TCONS_00020425 q1 q2 OK 0.01018440 41.0838
14718 TCONS_00014757 q1 q2 OK 0.01255110 52.7526
38909 TCONS_00038994 q1 q2 OK 0.00506554 18.4579
9364 TCONS_00009383 q1 q2 OK 0.01624700 41.5996
21567 TCONS_00021617 q1 q2 OK 0.02047770 43.5210
21617 TCONS_00021668 q1 q2 OK 0.07737150 173.5400
12908 TCONS_00012945 q1 q2 OK 0.01454510 29.1976
2916 TCONS_00002919 q1 q2 OK 0.02808040 52.5176
11888 TCONS_00011918 q1 q2 OK 0.01283370 23.4124
24967 TCONS_00025024 q1 q2 OK 0.07871780 93.7237
36578 TCONS_00036659 q1 q2 OK 0.15108000 179.3100
18827 TCONS_00018874 q1 q2 OK 0.19685300 402.2040
26748 TCONS_00026809 q1 q2 OK 0.07271350 66.3874
24573 TCONS_00024628 q1 q2 OK 0.01203420 20.7750
5805 TCONS_00005818 q1 q2 OK 0.00198928 2.9240
35808 TCONS_00035884 q1 q2 OK 0.10710700 108.1710
26864 TCONS_00026926 q1 q2 OK 0.05353970 86.0766
log2_fold_change test_stat p_value q_value significant
19598 15.45020 -7.91793 2.44249e-15 5.34124e-11 yes
23003 13.80210 -7.39372 1.42775e-13 1.56110e-09 yes
16085 12.66350 -7.33093 2.28484e-13 1.66550e-09 yes
20375 11.97800 -7.27264 3.52607e-13 1.92770e-09 yes
14718 12.03720 -7.23914 4.51417e-13 1.97432e-09 yes
38909 11.83120 -7.17187 7.39853e-13 2.69652e-09 yes
9364 11.32220 -6.84004 7.91722e-12 2.47334e-08 yes
21567 11.05340 -6.73898 1.59504e-11 3.87558e-08 yes
21617 11.13120 -6.75063 1.47207e-11 3.87558e-08 yes
12908 10.97110 -6.67956 2.39653e-11 5.24073e-08 yes
2916 10.86900 -6.61070 3.82498e-11 6.62383e-08 yes
11888 10.83310 -6.59542 4.24061e-11 6.62383e-08 yes
24967 10.21750 -6.60852 3.88183e-11 6.62383e-08 yes
36578 10.21290 -6.59690 4.19833e-11 6.62383e-08 yes
18827 10.99660 -6.54690 5.87441e-11 8.56411e-08 yes
26748 9.83447 -6.44433 1.16116e-10 1.58701e-07 yes
24573 10.75350 -6.42860 1.28785e-10 1.65663e-07 yes
5805 10.52150 -6.40323 1.52120e-10 1.84809e-07 yes
35808 9.98005 -6.39398 1.61620e-10 1.86017e-07 yes
26864 10.65080 -6.35030 2.14901e-10 2.34972e-07 yes


however, these top 20 include transcripts that start with NM_00000 and NR_00000

what I want is to select only the NM_ as these are proteins/transcript, NR_ if I am not wrong is the gene (here cummerbund only gives TCONS, but I have double checked themn with the NM/NR nomenclature and I know they are mixed up as it is listing by fold change...)

How do I command this on cummerbund?

thanks,
ibseq
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