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-   -   cummeRbund csScatter() error (http://seqanswers.com/forums/showthread.php?t=49722)

joseph 01-21-2015 03:32 PM

cummeRbund csScatter() error
 
Hello
Can you please help me find out why I am getting this error? Thanks

cuff = readCufflinks()
> cuff
CuffSet instance with:
3 samples
14017 genes
32101 isoforms
19668 TSS
18380 CDS
14017 promoters
39336 splicing
12808 relCDS

The functions csVolcanoMatrix() and csDensity() work fine, but the function csScatter() gives the following error:
Code:

> csScatter(genes(cuff))
Error in sqliteSendQuery(con, statement, bind.data) :
  error in statement: near "OR": syntax error

OR is the name of one of the 3 samples.


> sessionInfo()
R version 3.1.2 Patched (2015-01-19 r67548)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.6.8 (Snow Leopard)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] cummeRbund_2.8.2 Gviz_1.10.5 rtracklayer_1.26.2 GenomicRanges_1.18.4 GenomeInfoDb_1.2.4 IRanges_2.0.1 S4Vectors_0.4.0
[8] fastcluster_1.1.15 reshape2_1.4.1 ggplot2_1.0.0 RSQLite_1.0.0 DBI_0.3.1 BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 AnnotationDbi_1.28.1 base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8 Biobase_2.26.0
[7] BiocParallel_1.0.0 biomaRt_2.22.0 Biostrings_2.34.1 biovizBase_1.14.1 bitops_1.0-6 brew_1.0-6
[13] BSgenome_1.34.1 checkmate_1.5.1 cluster_1.15.3 codetools_0.2-10 colorspace_1.2-4 dichromat_2.0-0
[19] digest_0.6.8 fail_1.2 foreach_1.4.2 foreign_0.8-62 Formula_1.2-0 GenomicAlignments_1.2.1
[25] GenomicFeatures_1.18.3 gtable_0.1.2 Hmisc_3.14-6 iterators_1.0.7 labeling_0.3 lattice_0.20-29
[31] latticeExtra_0.6-26 MASS_7.3-37 matrixStats_0.12.2 munsell_0.4.2 nnet_7.3-8 plyr_1.8.1
[37] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.1-2 Rcpp_0.11.3 RCurl_1.95-4.5 rpart_4.1-8
[43] Rsamtools_1.18.2 scales_0.2.4 sendmailR_1.2-1 splines_3.1.2 stringr_0.6.2 survival_2.37-7
[49] tools_3.1.2 VariantAnnotation_1.12.8 XML_3.98-1.1 XVector_0.6.0 zlibbioc_1.12.0

TiborNagy 01-23-2015 04:44 AM

Maybe your sample name is conflicted with the SQL syntax. Try to add another name for your sample.

karimhasanpur@yahoo.com 06-07-2015 12:08 AM

cs.scattermatrix error
 
Quote:

Originally Posted by joseph (Post 158537)
Hello
Can you please help me find out why I am getting this error? Thanks

cuff = readCufflinks()
> cuff
CuffSet instance with:
3 samples
14017 genes
32101 isoforms
19668 TSS
18380 CDS
14017 promoters
39336 splicing
12808 relCDS

The functions csVolcanoMatrix() and csDensity() work fine, but the function csScatter() gives the following error:
Code:

> csScatter(genes(cuff))
Error in sqliteSendQuery(con, statement, bind.data) :
  error in statement: near "OR": syntax error

OR is the name of one of the 3 samples.


> sessionInfo()
R version 3.1.2 Patched (2015-01-19 r67548)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.6.8 (Snow Leopard)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] cummeRbund_2.8.2 Gviz_1.10.5 rtracklayer_1.26.2 GenomicRanges_1.18.4 GenomeInfoDb_1.2.4 IRanges_2.0.1 S4Vectors_0.4.0
[8] fastcluster_1.1.15 reshape2_1.4.1 ggplot2_1.0.0 RSQLite_1.0.0 DBI_0.3.1 BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 AnnotationDbi_1.28.1 base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8 Biobase_2.26.0
[7] BiocParallel_1.0.0 biomaRt_2.22.0 Biostrings_2.34.1 biovizBase_1.14.1 bitops_1.0-6 brew_1.0-6
[13] BSgenome_1.34.1 checkmate_1.5.1 cluster_1.15.3 codetools_0.2-10 colorspace_1.2-4 dichromat_2.0-0
[19] digest_0.6.8 fail_1.2 foreach_1.4.2 foreign_0.8-62 Formula_1.2-0 GenomicAlignments_1.2.1
[25] GenomicFeatures_1.18.3 gtable_0.1.2 Hmisc_3.14-6 iterators_1.0.7 labeling_0.3 lattice_0.20-29
[31] latticeExtra_0.6-26 MASS_7.3-37 matrixStats_0.12.2 munsell_0.4.2 nnet_7.3-8 plyr_1.8.1
[37] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.1-2 Rcpp_0.11.3 RCurl_1.95-4.5 rpart_4.1-8
[43] Rsamtools_1.18.2 scales_0.2.4 sendmailR_1.2-1 splines_3.1.2 stringr_0.6.2 survival_2.37-7
[49] tools_3.1.2 VariantAnnotation_1.12.8 XML_3.98-1.1 XVector_0.6.0 zlibbioc_1.12.0

Dear Jozeph,

I am now encountered with the same error as you were. Did you find a way to solve your problem? I would be so grateful if you share that with me.

Thanks in advance'
Karim


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