plotZScores error in FourCSeq
2
0
Entering edit mode
snowhune • 0
@snowhune-10152
Last seen 5.3 years ago

Dear,

In "plotZsocres(fcf)", I have a following error:

Error in print(tracks(plots, heights = heights, xlim = frags[abs(frags$dist) <  : 
  error in evaluating the argument 'x' in selecting a method for function 'print': Error: Objects of type standardGeneric not supported by autoplot.

 

And I got the same error with "plotDifferenes(fcf)".

I followed all the vignette procedure and I didn't have any other error.

my sessioninfo is:

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

locale:
[1] C

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

other attached packages:
 [1] BSgenome.Mmusculus.UCSC.mm9_1.4.0       BSgenome_1.38.0                         rtracklayer_1.30.3                  Biostrings_2.38.4                      
 [5] XVector_0.10.0                          ggbio_1.18.1                            BiocInstaller_1.20.1                    TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
 [9] GenomicFeatures_1.22.13                 AnnotationDbi_1.32.3                    FourCSeq_1.4.0                          LSD_3.0                                
[13] DESeq2_1.10.1                           RcppArmadillo_0.6.500.4.0               Rcpp_0.12.4                             SummarizedExperiment_1.0.2             
[17] Biobase_2.30.0                          ggplot2_2.1.0                           GenomicRanges_1.22.4                    GenomeInfoDb_1.6.3                     
[21] IRanges_2.4.8                           S4Vectors_0.8.11                        BiocGenerics_0.16.1                    

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.1           biovizBase_1.18.0        lattice_0.20-33          gtools_3.5.0             Rsamtools_1.22.0         plyr_1.8.3               futile.options_1.0.0    
 [8] acepack_1.3-3.3          RSQLite_1.0.0            zlibbioc_1.16.0          annotate_1.48.0          rpart_4.1-10             Matrix_1.2-4             BiocParallel_1.4.3      
[15] geneplotter_1.48.0       stringr_1.0.0            foreign_0.8-66           RCurl_1.95-4.8           biomaRt_2.26.1           munsell_0.4.3            nnet_7.3-12             
[22] gridExtra_2.2.1          Hmisc_3.17-2             XML_3.98-1.4             reshape_0.8.5            GenomicAlignments_1.6.3  bitops_1.0-6             RBGL_1.46.0             
[29] grid_3.2.3               xtable_1.8-2             GGally_1.0.1             gtable_0.2.0             DBI_0.3.1                magrittr_1.5             scales_0.4.0            
[36] graph_1.48.0             stringi_1.0-1            reshape2_1.4.1           genefilter_1.52.1        latticeExtra_0.6-28      futile.logger_1.4.1      Formula_1.2-1           
[43] lambda.r_1.1.7           RColorBrewer_1.1-2       tools_3.2.3              dichromat_2.0-0          OrganismDbi_1.12.1       survival_2.38-3          colorspace_1.2-6        
[50] cluster_2.0.3            fda_2.4.4                VariantAnnotation_1.16.4

fourCseq • 549 views
ADD COMMENT
0
Entering edit mode
felix.klein ▴ 150
@felixklein-6900
Last seen 3.1 years ago
Germany
Hello, its a bit hard to trace back the error from the information you provided. Could you also show summaries of the objects you have. Or provide a rdd file with the fcf object if it is not too big. Best regards, Felix Am Mi., Apr. 27, 2016 15:25 schrieb snowhune [bioc] : Activity on a post you are following on support.bioconductor.org (https://support.bioconductor.org) User snowhune (snowhune) wrote Question: plotZScores error in FourCSeq (https://support.bioconductor.org/p/81986/): Dear, In "plotZsocres(fcf)", I have a following error: Error in print(tracks(plots, heights = heights, xlim = frags[abs(frags$dist) < : error in evaluating the argument 'x' in selecting a method for function 'print': Error: Objects of type standardGeneric not supported by autoplot. And I got the same error with "plotDifferenes(fcf)". I followed all the vignette procedure and I didn't have any other error. my sessioninfo is: R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago) locale: [1] C attached base packages: [1] splines stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Mmusculus.UCSC.mm9_1.4.0 BSgenome_1.38.0 rtracklayer_1.30.3 Biostrings_2.38.4 [5] XVector_0.10.0 ggbio_1.18.1 BiocInstaller_1.20.1 TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 [9] GenomicFeatures_1.22.13 AnnotationDbi_1.32.3 FourCSeq_1.4.0 LSD_3.0 [13] DESeq2_1.10.1 RcppArmadillo_0.6.500.4.0 Rcpp_0.12.4 SummarizedExperiment_1.0.2 [17] Biobase_2.30.0 ggplot2_2.1.0 GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 [21] IRanges_2.4.8 S4Vectors_0.8.11 BiocGenerics_0.16.1 loaded via a namespace (and not attached): [1] locfit_1.5-9.1 biovizBase_1.18.0 lattice_0.20-33 gtools_3.5.0 Rsamtools_1.22.0 plyr_1.8.3 futile.options_1.0.0 [8] acepack_1.3-3.3 RSQLite_1.0.0 zlibbioc_1.16.0 annotate_1.48.0 rpart_4.1-10 Matrix_1.2-4 BiocParallel_1.4.3 [15] geneplotter_1.48.0 stringr_1.0.0 foreign_0.8-66 RCurl_1.95-4.8 biomaRt_2.26.1 munsell_0.4.3 nnet_7.3-12 [22] gridExtra_2.2.1 Hmisc_3.17-2 XML_3.98-1.4 reshape_0.8.5 GenomicAlignments_1.6.3 bitops_1.0-6 RBGL_1.46.0 [29] grid_3.2.3 xtable_1.8-2 GGally_1.0.1 gtable_0.2.0 DBI_0.3.1 magrittr_1.5 scales_0.4.0 [36] graph_1.48.0 stringi_1.0-1 reshape2_1.4.1 genefilter_1.52.1 latticeExtra_0.6-28 futile.logger_1.4.1 Formula_1.2-1 [43] lambda.r_1.1.7 RColorBrewer_1.1-2 tools_3.2.3 dichromat_2.0-0 OrganismDbi_1.12.1 survival_2.38-3 colorspace_1.2-6 [50] cluster_2.0.3 fda_2.4.4 VariantAnnotation_1.16.4 ------------------------------------ Post tags: fourCseq You may reply via email or visit plotZScores error in FourCSeq (plotZScores error in FourCSeq)
ADD COMMENT
0
Entering edit mode
snowhune • 0
@snowhune-10152
Last seen 5.3 years ago

For those who may have an interest on this issue,

We (I and Felix) figured out that it was due to the R version problem. Some functions related to graph requires more latest version that I used.

With R3.3.0, FourCSeq1.6 version and recent updates on related packages, there was no problem on plotting.

Thanks Felix

ADD COMMENT

Login before adding your answer.

Traffic: 500 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6