warnings
ama2241 opened this issue · 1 comments
Hi There,
Thank you for this amazing tool you have created for RNAseq data analysis. I just want to bring to your attention a few warnings I noticed. I don't believe this might have resulted in any issues with the data analysis:
After the step:
exploreCounts(object=out.DESeq2$dds, group=target[,varInt], typeTrans=typeTrans, col=colors)
I get this:
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
null device
1
Warning message:
expand_scale() is deprecated; use expansion() instead.
When I use the code:
warnings()
Warning messages:
1: expand_scale() is deprecated; use expansion() instead.
2: expand_scale() is deprecated; use expansion() instead.
3: expand_scale() is deprecated; use expansion() instead.
4: expand_scale() is deprecated; use expansion() instead.
5: expand_scale() is deprecated; use expansion() instead.
6: expand_scale() is deprecated; use expansion() instead.
7: expand_scale() is deprecated; use expansion() instead.
8: expand_scale() is deprecated; use expansion() instead.
9: expand_scale() is deprecated; use expansion() instead.
10: expand_scale() is deprecated; use expansion() instead.
11: expand_scale() is deprecated; use expansion() instead.
12: expand_scale() is deprecated; use expansion() instead.
13: expand_scale() is deprecated; use expansion() instead.
14: expand_scale() is deprecated; use expansion() instead.
15: expand_scale() is deprecated; use expansion() instead.
16: expand_scale() is deprecated; use expansion() instead.
17: expand_scale() is deprecated; use expansion() instead.
18: expand_scale() is deprecated; use expansion() instead.
19: expand_scale() is deprecated; use expansion() instead.
20: expand_scale() is deprecated; use expansion() instead.
21: expand_scale() is deprecated; use expansion() instead.
22: expand_scale() is deprecated; use expansion() instead.
23: expand_scale() is deprecated; use expansion() instead.
24: expand_scale() is deprecated; use expansion() instead.
25: expand_scale() is deprecated; use expansion() instead.
26: expand_scale() is deprecated; use expansion() instead.
27: expand_scale() is deprecated; use expansion() instead.
28: expand_scale() is deprecated; use expansion() instead.
29: expand_scale() is deprecated; use expansion() instead.
30: expand_scale() is deprecated; use expansion() instead.
31: expand_scale() is deprecated; use expansion() instead.
32: expand_scale() is deprecated; use expansion() instead.
33: expand_scale() is deprecated; use expansion() instead.
34: expand_scale() is deprecated; use expansion() instead.
35: expand_scale() is deprecated; use expansion() instead.
Below is my session info:
sessionInfo()
**R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] SARTools_1.7.2 kableExtra_1.1.0
[3] ggplot2_3.3.0 edgeR_3.28.1
[5] limma_3.42.2 DESeq2_1.26.0
[7] SummarizedExperiment_1.16.1 DelayedArray_0.12.3
[9] BiocParallel_1.20.1 matrixStats_0.56.0
[11] Biobase_2.46.0 GenomicRanges_1.38.0
[13] GenomeInfoDb_1.22.1 IRanges_2.20.2
[15] S4Vectors_0.24.4 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 bit64_0.9-7 webshot_0.5.2
[4] RColorBrewer_1.1-2 httr_1.4.1 tools_3.6.3
[7] backports_1.1.6 R6_2.4.1 rpart_4.1-15
[10] Hmisc_4.4-0 DBI_1.1.0 colorspace_1.4-1
[13] nnet_7.3-13 withr_2.1.2 GGally_1.5.0
[16] gridExtra_2.3 bit_1.1-15.2 compiler_3.6.3
[19] cli_2.0.2 rvest_0.3.5 htmlTable_1.13.3
[22] xml2_1.3.1 ggdendro_0.1-20 labeling_0.3
[25] scales_1.1.0 checkmate_2.0.0 readr_1.3.1
[28] genefilter_1.68.0 stringr_1.4.0 digest_0.6.25
[31] foreign_0.8-76 rmarkdown_2.1 XVector_0.26.0
[34] base64enc_0.1-3 jpeg_0.1-8.1 pkgconfig_2.0.3
[37] htmltools_0.4.0 highr_0.8 htmlwidgets_1.5.1
[40] rlang_0.4.5 rstudioapi_0.11 RSQLite_2.2.0
[43] farver_2.0.3 acepack_1.4.1 RCurl_1.98-1.1
[46] magrittr_1.5 GenomeInfoDbData_1.2.2 Formula_1.2-3
[49] Matrix_1.2-18 Rcpp_1.0.4.6 munsell_0.5.0
[52] fansi_0.4.1 lifecycle_0.2.0 yaml_2.2.1
[55] stringi_1.4.6 MASS_7.3-51.5 zlibbioc_1.32.0
[58] plyr_1.8.6 grid_3.6.3 blob_1.2.1
[61] ggrepel_0.8.2 crayon_1.3.4 lattice_0.20-41
[64] splines_3.6.3 annotate_1.64.0 hms_0.5.3
[67] locfit_1.5-9.4 knitr_1.28 pillar_1.4.3
[70] geneplotter_1.64.0 XML_3.99-0.3 glue_1.4.0
[73] evaluate_0.14 latticeExtra_0.6-29 data.table_1.12.8
[76] png_0.1-7 vctrs_0.2.4 gtable_0.3.0
[79] reshape_0.8.8 assertthat_0.2.1 xfun_0.13
[82] xtable_1.8-4 survival_3.1-12 viridisLite_0.3.0
[85] tibble_3.0.0 AnnotationDbi_1.48.0 memoise_1.1.0
[88] cluster_2.1.0 ellipsis_0.3.0**