pedrostrusso
commented
4 years ago Hi, @CDaems thanks for using CEMiTool!
I'm not sure what might be causing the error you're having, but you could try setting the plot_diagnostics argument to FALSE, or the plot argument to FALSE, or both, and you should be able to get away with it. On the other hand, we don't really recommend running CEMiTool with only 11 samples, an ideal amount would be around at the very least 18.
Hi,
I'm new to using R for data analysis and just managed to perform DESeq2 on my RNA-sequencing data. I would like to use cemitool, but I keep on getting the same error:
Error in dev.off() : cannot shut down device 1 (the null device)Previously everything worked fine, and performing cemitool on the data that is included in the package works (expr0) fine as well. The code that I've used is the following:
`> library(CEMiTool)
Expr: contains 11 samples with 15679 variables. This data is normalized data that I've obtained using DESeq2 ann: is my annotation file, containing SampleName column stating the different samples + Class with the genotype of my animals.
I have already tried to update RStudio, restart it for a couple of times and tried to work in R instead of RStudio. But I keep on having the same issue. Underneath you can find the sessionInfo().
Could you please help me with this issue, as I have no clue what to do or what I'm doing wrong.
Many thanks in advance, Carmen
`> sessionInfo() R version 3.5.3 (2019-03-11) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale: [1] LC_COLLATE=Dutch_Belgium.1252 LC_CTYPE=Dutch_Belgium.1252 LC_MONETARY=Dutch_Belgium.1252 [4] LC_NUMERIC=C LC_TIME=Dutch_Belgium.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] CEMiTool_1.6.11
loaded via a namespace (and not attached): [1] backports_1.1.4 Hmisc_4.2-0 fastmatch_1.1-0
[4] plyr_1.8.4 igraph_1.2.4.1 lazyeval_0.2.2
[7] splines_3.5.3 BiocParallel_1.16.6 GenomeInfoDb_1.18.2
[10] ggplot2_3.2.0 urltools_1.7.3 robust_0.4-18.1
[13] digest_0.6.20 foreach_1.4.7 htmltools_0.3.6
[16] GOSemSim_2.8.0 viridis_0.5.1 GO.db_3.7.0
[19] ggpmisc_0.3.1 gdata_2.18.0 magrittr_1.5
[22] checkmate_1.9.4 memoise_1.1.0 fit.models_0.5-14
[25] cluster_2.0.7-1 doParallel_1.0.15 limma_3.38.3
[28] sna_2.4 fastcluster_1.1.25 annotate_1.60.1
[31] matrixStats_0.54.0 GeneOverlap_1.18.0 enrichplot_1.2.0
[34] prettyunits_1.0.2 colorspace_1.4-1 blob_1.2.0
[37] rrcov_1.4-7 ggrepel_0.8.1 xfun_0.8
[40] dplyr_0.8.3 crayon_1.3.4 RCurl_1.95-4.12
[43] jsonlite_1.6 graph_1.60.0 ffbase_0.12.7
[46] genefilter_1.64.0 zeallot_0.1.0 impute_1.56.0
[49] survival_2.43-3 iterators_1.0.12 glue_1.3.1
[52] polyclip_1.10-0 gtable_0.3.0 zlibbioc_1.28.0
[55] XVector_0.22.0 UpSetR_1.4.0 DelayedArray_0.8.0
[58] gRbase_1.8-3.4 BiocGenerics_0.28.0 DEoptimR_1.0-8
[61] scales_1.0.0 DOSE_3.8.2 mvtnorm_1.0-11
[64] DBI_1.0.0 ggthemes_4.2.0 Rcpp_1.0.2
[67] viridisLite_0.3.0 xtable_1.8-4 progress_1.2.2
[70] htmlTable_1.13.1 gridGraphics_0.4-1 foreign_0.8-71
[73] bit_1.1-14 europepmc_0.3 preprocessCore_1.44.0
[76] Formula_1.2-3 stats4_3.5.3 DT_0.8
[79] htmlwidgets_1.3 httr_1.4.1 fgsea_1.8.0
[82] gplots_3.0.1.1 RColorBrewer_1.1-2 acepack_1.4.1
[85] ff_2.2-14 pkgconfig_2.0.2 XML_3.98-1.20
[88] farver_1.1.0 nnet_7.3-12 locfit_1.5-9.1
[91] dynamicTreeCut_1.63-1 polynom_1.4-0 labeling_0.3
[94] ggplotify_0.0.4 tidyselect_0.2.5 rlang_0.4.0
[97] reshape2_1.4.3 AnnotationDbi_1.44.0 munsell_0.5.0
[100] tools_3.5.3 RSQLite_2.1.2 statnet.common_4.3.0
[103] ggridges_0.5.1 evaluate_0.14 stringr_1.4.0
[106] ggdendro_0.1-20 yaml_2.2.0 knitr_1.24
[109] bit64_0.9-7 robustbase_0.93-5 caTools_1.17.1.2
[112] purrr_0.3.2 ggraph_1.0.2 RBGL_1.58.2
[115] pracma_2.2.5 xml2_1.2.1 DO.db_2.9
[118] compiler_3.5.3 rstudioapi_0.10 tibble_2.1.3
[121] tweenr_1.0.1 geneplotter_1.60.0 pcaPP_1.9-73
[124] stringi_1.4.3 lattice_0.20-38 Matrix_1.2-15
[127] vctrs_0.2.0 pillar_1.4.2 BiocManager_1.30.4
[130] triebeard_0.3.0 data.table_1.12.2 cowplot_1.0.0
[133] bitops_1.0-6 GenomicRanges_1.34.0 qvalue_2.14.1
[136] R6_2.4.0 latticeExtra_0.6-28 network_1.15
[139] KernSmooth_2.23-15 gridExtra_2.3 IRanges_2.16.0
[142] codetools_0.2-16 MASS_7.3-51.1 gtools_3.8.1
[145] assertthat_0.2.1 SummarizedExperiment_1.12.0 DESeq2_1.22.2
[148] S4Vectors_0.20.1 GenomeInfoDbData_1.2.0 intergraph_2.0-2
[151] parallel_3.5.3 hms_0.5.0 clusterProfiler_3.10.1
[154] grid_3.5.3 rpart_4.1-13 coda_0.19-3
[157] tidyr_0.8.3 rmarkdown_1.14 rvcheck_0.1.3
[160] ggforce_0.2.2 Biobase_2.42.0 WGCNA_1.68
[163] base64enc_0.1-3 `