[Bug Report] pvalue of zero are no longer transform to the machine minimum number MAC M1

[rLannes]

Hi,

In my case, pvalues of 0 are transformed to the minimum pvalue of my list, no longer the minimum number R will represent (1e-308)

sesseionInfo()

sessionInfo() R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.3

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] dplyr_1.1.1 EnhancedVolcano_1.16.0 ggrepel_0.9.3 ggplot2_3.4.2

loaded via a namespace (and not attached): [1] Rcpp_1.0.10 fansi_1.0.4 withr_2.5.0 utf8_1.2.3 grid_4.2.2 R6_2.5.1 lifecycle_1.0.3 [8] gtable_0.3.3 magrittr_2.0.3 scales_1.2.1 pillar_1.9.0 rlang_1.1.0 cli_3.6.1 farver_2.1.1
[15] rstudioapi_0.14 generics_0.1.3 vctrs_0.6.1 labeling_0.4.2 tools_4.2.2 glue_1.6.2 munsell_0.5.0
[22] compiler_4.2.2 pkgconfig_2.0.3 colorspace_2.1-0 tidyselect_1.2.0 tibble_3.2.1

[guidohooiveld]

AFAIK this is intended behavior; note that this has been changed since v1.2.1 and higher:

https://github.com/kevinblighe/EnhancedVolcano/commit/606cdc3c9b98e36fd2086d92bdf61ec27b715015

Quote:

• New functionality in > v1.2:
• Now convert to 10^-1 lower than lowest non-zero p-value

Indeed, before v1.2.1 p-values were converted into the machine-lowest value possible (.Machine$double.xmin)

https://github.com/kevinblighe/EnhancedVolcano/blob/7abca284367c4146524397e0bb056fc231a095df/R/EnhancedVolcano.R#L314-L335

[rLannes]

Thank you for the clarification, I have missed that!

Best regards, Romain