Thank you for developing and maintaining this usefull tool.
scripts.R.txt
wes_turoeial.log.txt
Describe the bug
I cannot get the same result following the tutorial. I wonder if it's my R version causes the error. I attached the scripts I used and print out in the log file. The resulted lambda should be around 1 but mine is 66.24. And the alpha is Inf.
I wonder if this warning needs a particular attention: In glm(formula, data = as.data.frame(tdt), family = poisson) : fitting to calculate the null deviance did not converge -- increase 'maxit'?
Below is my R session info:
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.10 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /apps/intel-oneapi/mkl/2023.2.0/lib/intel64/libmkl_intel_lp64.so.2; LAPACK version 3.10.1
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
time zone: :/etc/localtime
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] MASS_7.3-60 rtracklayer_1.60.1 gTrack_0.1.0
[4] fishHook_0.1 data.table_1.17.2 plotly_4.10.4
[7] ggplot2_3.5.1 gUtils_0.2.0 GenomicRanges_1.52.1
[10] GenomeInfoDb_1.36.4 IRanges_2.34.1 S4Vectors_0.38.2
[13] BiocGenerics_0.46.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.30.2 gtable_0.3.6
[3] rjson_0.2.23 htmlwidgets_1.6.4
[5] Biobase_2.60.0 lattice_0.21-8
[7] vctrs_0.6.5 tools_4.3.1
[9] bitops_1.0-9 generics_0.1.3
[11] parallel_4.3.1 tibble_3.2.1
[13] pkgconfig_2.0.3 Matrix_1.5-4.1
[15] lifecycle_1.0.4 GenomeInfoDbData_1.2.10
[17] compiler_4.3.1 stringr_1.5.1
[19] Rsamtools_2.16.0 Biostrings_2.68.1
[21] munsell_0.5.1 codetools_0.2-19
[23] htmltools_0.5.8.1 RCurl_1.98-1.17
[25] yaml_2.3.10 lazyeval_0.2.2
[27] pillar_1.10.2 crayon_1.5.3
[29] tidyr_1.3.1 BiocParallel_1.34.2
[31] DelayedArray_0.26.7 abind_1.4-8
[33] tidyselect_1.2.1 digest_0.6.37
[35] stringi_1.8.7 dplyr_1.1.4
[37] purrr_1.0.4 restfulr_0.0.15
[39] fastmap_1.2.0 grid_4.3.1
[41] colorspace_2.1-1 cli_3.6.4
[43] magrittr_2.0.3 S4Arrays_1.0.6
[45] XML_3.99-0.18 withr_3.0.2
[47] scales_1.3.0 XVector_0.40.0
[49] httr_1.4.7 matrixStats_1.5.0
[51] zoo_1.8-13 BiocIO_1.10.0
[53] viridisLite_0.4.2 rlang_1.1.5
[55] glue_1.8.0 jsonlite_2.0.0
[57] R6_2.6.1 MatrixGenerics_1.12.3
[59] GenomicAlignments_1.36.0 zlibbioc_1.46.0
Thank you for developing and maintaining this usefull tool.
scripts.R.txt
wes_turoeial.log.txt
Describe the bug
I cannot get the same result following the tutorial. I wonder if it's my R version causes the error. I attached the scripts I used and print out in the log file. The resulted lambda should be around 1 but mine is 66.24. And the alpha is Inf.
I wonder if this warning needs a particular attention:
In glm(formula, data = as.data.frame(tdt), family = poisson) : fitting to calculate the null deviance did not converge -- increase 'maxit'?Below is my R session info:
Matrix products: default
BLAS/LAPACK: /apps/intel-oneapi/mkl/2023.2.0/lib/intel64/libmkl_intel_lp64.so.2; LAPACK version 3.10.1
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
time zone: :/etc/localtime
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] MASS_7.3-60 rtracklayer_1.60.1 gTrack_0.1.0
[4] fishHook_0.1 data.table_1.17.2 plotly_4.10.4
[7] ggplot2_3.5.1 gUtils_0.2.0 GenomicRanges_1.52.1
[10] GenomeInfoDb_1.36.4 IRanges_2.34.1 S4Vectors_0.38.2
[13] BiocGenerics_0.46.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.30.2 gtable_0.3.6
[3] rjson_0.2.23 htmlwidgets_1.6.4
[5] Biobase_2.60.0 lattice_0.21-8
[7] vctrs_0.6.5 tools_4.3.1
[9] bitops_1.0-9 generics_0.1.3
[11] parallel_4.3.1 tibble_3.2.1
[13] pkgconfig_2.0.3 Matrix_1.5-4.1
[15] lifecycle_1.0.4 GenomeInfoDbData_1.2.10
[17] compiler_4.3.1 stringr_1.5.1
[19] Rsamtools_2.16.0 Biostrings_2.68.1
[21] munsell_0.5.1 codetools_0.2-19
[23] htmltools_0.5.8.1 RCurl_1.98-1.17
[25] yaml_2.3.10 lazyeval_0.2.2
[27] pillar_1.10.2 crayon_1.5.3
[29] tidyr_1.3.1 BiocParallel_1.34.2
[31] DelayedArray_0.26.7 abind_1.4-8
[33] tidyselect_1.2.1 digest_0.6.37
[35] stringi_1.8.7 dplyr_1.1.4
[37] purrr_1.0.4 restfulr_0.0.15
[39] fastmap_1.2.0 grid_4.3.1
[41] colorspace_2.1-1 cli_3.6.4
[43] magrittr_2.0.3 S4Arrays_1.0.6
[45] XML_3.99-0.18 withr_3.0.2
[47] scales_1.3.0 XVector_0.40.0
[49] httr_1.4.7 matrixStats_1.5.0
[51] zoo_1.8-13 BiocIO_1.10.0
[53] viridisLite_0.4.2 rlang_1.1.5
[55] glue_1.8.0 jsonlite_2.0.0
[57] R6_2.6.1 MatrixGenerics_1.12.3
[59] GenomicAlignments_1.36.0 zlibbioc_1.46.0