Question: Vidger library error
0
gravatar for sbbinfo90
4 months 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!

vidger • 134 views
ADD COMMENTlink written 4 months 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 months ago • written 4 months ago by shepherl ♦♦ 1.1k

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 months 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 months 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 months ago by sbbinfo900
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 317 users visited in the last hour