Vidger library error
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sbbinfo90 • 0
@sbbinfo90-17078
Last seen 5.6 years ago

Hello,

I am using VIDGER from bioconductor but it shows an error:

vsMAMatrix(data = cuffdiffdata, d.factor = NULL, type='cuffdiff',padj = 0.05, y.lim = NULL, lfc = NULL, title = TRUE, legend = TRUE,grid = TRUE, counts = TRUError in `$<-.data.frame`(`*tmp*`, "id_x", value = "24hpi") : 

 replacement has 1 row, data has 0

Please reply with appropriate solution.

Thanks!

vidger • 824 views
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It would be also helpful for the pathview maintainers if you included your sessionInfo() so they are aware what os system, version of R, and version of the package you are using.

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Sure,

> sessionInfo()

R version 3.5.1 (2018-07-02)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS Linux 7 (Core)

Matrix products: default

BLAS: /home/sbharti/Softwares/R_351/lib64/R/lib/libRblas.so

LAPACK: /home/sbharti/Softwares/R_351/lib64/R/lib/libRlapack.so

locale:

 [1] LC_CTYPE=C                 LC_NUMERIC=C              

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

[1] vidger_1.1.4

 

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loaded via a namespace (and not attached):

 [1] Biobase_2.41.2              tidyr_0.8.1                

 [3] edgeR_3.23.3                bit64_0.9-7                

 [5] splines_3.5.1               Formula_1.2-3              

 [7] assertthat_0.2.0            stats4_3.5.1               

 [9] latticeExtra_0.6-28         blob_1.1.1                 

[11] GenomeInfoDbData_1.1.0      ggrepel_0.8.0              

[13] pillar_1.3.0                RSQLite_2.1.1              

[15] backports_1.1.2             lattice_0.20-35            

[17] limma_3.37.4                glue_1.3.0                 

[19] digest_0.6.17               GenomicRanges_1.33.13      

[21] RColorBrewer_1.1-2          XVector_0.21.3             

[23] checkmate_1.8.5             colorspace_1.3-2           

[25] htmltools_0.3.6             Matrix_1.2-14              

[27] plyr_1.8.4                  DESeq2_1.21.21             

[29] XML_3.98-1.16               pkgconfig_2.0.2            

[31] genefilter_1.63.2           zlibbioc_1.27.0            

[33] purrr_0.2.5                 xtable_1.8-3               

[35] scales_1.0.0                BiocParallel_1.15.12       

[37] htmlTable_1.12              tibble_1.4.2               

 

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[39] annotate_1.59.1             IRanges_2.15.17            

[41] ggplot2_3.0.0               SummarizedExperiment_1.11.6

[43] nnet_7.3-12                 BiocGenerics_0.27.1        

[45] lazyeval_0.2.1              survival_2.42-6            

[47] magrittr_1.5                crayon_1.3.4               

[49] evaluate_0.11               memoise_1.1.0              

[51] GGally_1.4.0                foreign_0.8-71             

[53] tools_3.5.1                 data.table_1.11.4          

[55] matrixStats_0.54.0          stringr_1.3.1              

[57] S4Vectors_0.19.19           locfit_1.5-9.1             

[59] munsell_0.5.0               cluster_2.0.7-1            

[61] DelayedArray_0.7.41         AnnotationDbi_1.43.1       

[63] bindrcpp_0.2.2              compiler_3.5.1             

[65] GenomeInfoDb_1.17.1         rlang_0.2.2                

[67] grid_3.5.1                  RCurl_1.95-4.11            

[69] rstudioapi_0.7              htmlwidgets_1.2            

[71] rmarkdown_1.10              bitops_1.0-6               

[73] base64enc_0.1-3             gtable_0.2.0               

[75] reshape_0.8.7               DBI_1.0.0                  

[77] R6_2.2.2                    gridExtra_2.3              

[79] knitr_1.20                  dplyr_0.7.6                

[81] bit_1.1-14                  rprojroot_1.3-2            

[83] bindr_0.1.1                 Hmisc_4.1-1                

[85] stringi_1.2.4               parallel_3.5.1             

[87] Rcpp_0.12.18                geneplotter_1.59.0         

[89] rpart_4.1-13                acepack_1.4.1              

[91] tidyselect_0.2.4 

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