Closed jhranitz closed 1 year ago
can you try turning the tibble into a data frame via as.data.frame()
? I think that might be the issue here
Thank you! Will do today. Do the geneIDs need to be in the HUGO gene nomenclature?
From: Ege Ulgen @.> Sent: Sunday, February 5, 2023 9:10 AM To: egeulgen/pathfindR @.> Cc: Hranitz, John M @.>; Author @.> Subject: Re: [egeulgen/pathfindR] Error in input_testing(sig_EtOH_data, 0.05) : p values must all be numeric (Issue #155)
can you try turning the tibble into a data frame via as.data.frame()? I think that might be the issue here
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For the default PIN and gene sets data, yes the ids should be gene symbols. You can use other types of ids as long as you keep the PIN and gene sets consistent.-EOn 5 Feb 2023, at 17:18, jhranitz @.***> wrote: Thank you! Will do today. Do the geneIDs need to be in the HUGO gene nomenclature?
From: Ege Ulgen @.> Sent: Sunday, February 5, 2023 9:10 AM To: egeulgen/pathfindR @.> Cc: Hranitz, John M @.>; Author @.> Subject: Re: [egeulgen/pathfindR] Error in input_testing(sig_EtOH_data, 0.05) : p values must all be numeric (Issue #155)
can you try turning the tibble into a data frame via as.data.frame()? I think that might be the issue here
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Very grateful for the fix. Thank you - this fixed the issue with the data recognition. Now on to trouble-shooting on the PIN. My apologies, I'm not trained in bioinformatics... old dog learning some new tricks.
Cheers, John
From: Ege Ulgen @.> Sent: Sunday, February 5, 2023 12:00 PM To: egeulgen/pathfindR @.> Cc: Hranitz, John M @.>; Author @.> Subject: Re: [egeulgen/pathfindR] Error in input_testing(sig_EtOH_data, 0.05) : p values must all be numeric (Issue #155)
For the default PIN and gene sets data, yes the ids should be gene symbols. You can use other types of ids as long as you keep the PIN and gene sets consistent.-EOn 5 Feb 2023, at 17:18, jhranitz @.***> wrote: Thank you! Will do today. Do the geneIDs need to be in the HUGO gene nomenclature?
From: Ege Ulgen @.> Sent: Sunday, February 5, 2023 9:10 AM To: egeulgen/pathfindR @.> Cc: Hranitz, John M @.>; Author @.> Subject: Re: [egeulgen/pathfindR] Error in input_testing(sig_EtOH_data, 0.05) : p values must all be numeric (Issue #155)
can you try turning the tibble into a data frame via as.data.frame()? I think that might be the issue here
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I receive the error: "Error in input_testing(sig_EtOH_data, 0.05) : p values must all be numeric" when I test the input to pathfindR.
visualize data structure
str(sig_EtOH_data)
test input data
input_testing(sig_EtOH_data, 0.05)
tibble [384 × 3] (S3: tbl_df/tbl/data.frame) $ geneID : num [1:384] 406078 406081 406091 406092 406093 ... $ logFC : num [1:384] 0.769 3.141 4.799 0.401 0.534 ... $ adj.P.Val: num [1:384] 4.61e-02 3.55e-04 6.44e-07 3.02e-02 3.10e-02 ...
Desktop (please complete the following information):
R Session Information:
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] readxl_1.4.1 pathfindR_1.6.4 pathfindR.data_1.1.3
loaded via a namespace (and not attached): [1] ggrepel_0.9.2 Rcpp_1.0.9 tidyr_1.2.1
[4] png_0.1-8 ps_1.7.2 Biostrings_2.66.0
[7] pak_0.4.0 assertthat_0.2.1 digest_0.6.31
[10] foreach_1.5.2 utf8_1.2.2 ggforce_0.4.1
[13] GenomeInfoDb_1.34.8 R6_2.5.1 cellranger_1.1.0
[16] stats4_4.2.2 evaluate_0.19 httr_1.4.4
[19] ggplot2_3.4.0 pillar_1.8.1 zlibbioc_1.44.0
[22] rlang_1.0.6 curl_4.3.3 rstudioapi_0.14
[25] callr_3.7.3 S4Vectors_0.36.1 rmarkdown_2.19
[28] RCurl_1.98-1.10 igraph_1.3.5 polyclip_1.10-4
[31] munsell_0.5.0 compiler_4.2.2 xfun_0.36
[34] pkgconfig_2.0.3 BiocGenerics_0.44.0 htmltools_0.5.4
[37] tidyselect_1.2.0 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9 [40] tibble_3.1.8 gridExtra_2.3 IRanges_2.32.0
[43] codetools_0.2-18 graphlayouts_0.8.4 fansi_1.0.3
[46] viridisLite_0.4.1 crayon_1.5.2 dplyr_1.0.10
[49] withr_2.5.0 bitops_1.0-7 MASS_7.3-58.1
[52] grid_4.2.2 gtable_0.3.1 lifecycle_1.0.3
[55] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
[58] cli_3.5.0 farver_2.1.1 XVector_0.38.0
[61] viridis_0.6.2 doParallel_1.0.17 generics_0.1.3
[64] vctrs_0.5.1 iterators_1.0.14 tools_4.2.2
[67] glue_1.6.2 tweenr_2.0.2 purrr_1.0.0
[70] ggraph_2.1.0 processx_3.8.0 parallel_4.2.2
[73] fastmap_1.1.0 colorspace_2.0-3 tidygraph_1.2.2
[76] knitr_1.41
Additional context data are from experiment investigating effect of ethanol intoxication on honey bee (Apis mellifera), logFC from microarrays.
Is this a geneID issue? Does the geneID need to be converted?