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Question: Vidger library error
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gravatar for sbbinfo90
8 days ago by
sbbinfo900
sbbinfo900 wrote:

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!

ADD COMMENTlink written 8 days ago by sbbinfo900

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.

ADD REPLYlink modified 4 days ago • written 4 days ago by shepherl ♦♦ 730

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

 

ADD REPLYlink written 4 days ago by sbbinfo900

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               

 

ADD REPLYlink written 4 days ago by sbbinfo900

[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 

ADD REPLYlink written 4 days ago by sbbinfo900
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