SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Help with CummeRbund error.. I'm lost beeman RNA Sequencing 0 08-31-2014 05:54 PM
CummeRbund error steindorff Bioinformatics 6 07-30-2013 05:37 AM
CummeRbund error NRiddiford RNA Sequencing 5 07-26-2013 11:18 AM
cummeRbund error emolinari Bioinformatics 0 06-15-2013 10:41 AM
CummeRbund error newbietonextgen Bioinformatics 1 06-15-2012 11:24 AM

Reply
 
Thread Tools
Old 01-21-2015, 03:32 PM   #1
joseph
Member
 
Location: ca

Join Date: Feb 2008
Posts: 39
Default 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
joseph is offline   Reply With Quote
Old 01-23-2015, 04:44 AM   #2
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

Maybe your sample name is conflicted with the SQL syntax. Try to add another name for your sample.
TiborNagy is offline   Reply With Quote
Old 06-07-2015, 12:08 AM   #3
karimhasanpur@yahoo.com
Junior Member
 
Location: Iran

Join Date: Nov 2013
Posts: 4
Default cs.scattermatrix error

Quote:
Originally Posted by joseph View Post
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
karimhasanpur@yahoo.com is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:08 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO