search

egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
Other
178 stars 25 forks source link

Error in input_testing(sig_EtOH_data, 0.05) : p values must all be numeric #155

Closed jhranitz closed 1 year ago

jhranitz commented 1 year ago

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.

  1. Prepared input as a data frame is three columns: geneID (numeric), logFC, adj_P_Value
  2. ran code:

visualize data structure

str(sig_EtOH_data)

test input data

input_testing(sig_EtOH_data, 0.05)

  1. output received was:

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 ...

test input data

input_testing(sig_EtOH_data, 0.05) Error in input_testing(sig_EtOH_data, 0.05) : p values must all be numeric

Desktop (please complete the following information):

R Session Information:

sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Ventura 13.1

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?

egeulgen commented 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

jhranitz commented 1 year ago

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

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.com/v3/__https://github.com/egeulgen/pathfindR/issues/155*issuecomment-1417946598__;Iw!!I1GahPdV!ZUsIH2iTeNLscBMrS0bfnWLywOe_SIRJ2_m5d5i7bJ9qAMqhg6Ldo7bB8e2PEv1XXR8CDTILQgVd6TGT9Ab8kinStEIk_ZiG$, or unsubscribe [github.com]https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A5VBZWBTFEVTMDKSNV47F3TWV6YETANCNFSM6AAAAAAUQTASXQ__;!!I1GahPdV!ZUsIH2iTeNLscBMrS0bfnWLywOe_SIRJ2_m5d5i7bJ9qAMqhg6Ldo7bB8e2PEv1XXR8CDTILQgVd6TGT9Ab8kinStEXDguWt$. You are receiving this because you authored the thread.Message ID: @.***>

egeulgen commented 1 year ago

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

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.com/v3/__https://github.com/egeulgen/pathfindR/issues/155*issuecomment-1417946598__;Iw!!I1GahPdV!ZUsIH2iTeNLscBMrS0bfnWLywOe_SIRJ2_m5d5i7bJ9qAMqhg6Ldo7bB8e2PEv1XXR8CDTILQgVd6TGT9Ab8kinStEIk_ZiG$, or unsubscribe [github.com]https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A5VBZWBTFEVTMDKSNV47F3TWV6YETANCNFSM6AAAAAAUQTASXQ__;!!I1GahPdV!ZUsIH2iTeNLscBMrS0bfnWLywOe_SIRJ2_m5d5i7bJ9qAMqhg6Ldo7bB8e2PEv1XXR8CDTILQgVd6TGT9Ab8kinStEXDguWt$. You are receiving this because you authored the thread.Message ID: @.***>

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: @.***>

jhranitz commented 1 year ago

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

— Reply to this email directly, view it on GitHub [github.com]<https://urldefense.com/v3/__https://github.com/egeulgen/pathfindR/issues/155*issuecomment-1417946598__;Iw!!I1GahPdV!ZUsIH2iTeNLscBMrS0bfnWLywOe_SIRJ2_m5d5i7bJ9qAMqhg6Ldo7bB8e2PEv1XXR8CDTILQgVd6TGT9Ab8kinStEIk_ZiG$%3E, or unsubscribe [github.com]<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A5VBZWBTFEVTMDKSNV47F3TWV6YETANCNFSM6AAAAAAUQTASXQ__;!!I1GahPdV!ZUsIH2iTeNLscBMrS0bfnWLywOe_SIRJ2_m5d5i7bJ9qAMqhg6Ldo7bB8e2PEv1XXR8CDTILQgVd6TGT9Ab8kinStEXDguWt$%3E. You are receiving this because you authored the thread.Message ID: @.***>

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.com/v3/__https://github.com/egeulgen/pathfindR/issues/155*issuecomment-1418157449__;Iw!!I1GahPdV!db5-QIVjWLqEzM1KYf9FV2eIo9fERYmmfkpGx7utLiwz32AlDIed46hnHNZJVKfGFSv6EG0HBxwaDC9rLHpfafG5SkeRMuE_$, or unsubscribe [github.com]https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A5VBZWCJ3U6EPCPUL5EI2XDWV7MERANCNFSM6AAAAAAUQTASXQ__;!!I1GahPdV!db5-QIVjWLqEzM1KYf9FV2eIo9fERYmmfkpGx7utLiwz32AlDIed46hnHNZJVKfGFSv6EG0HBxwaDC9rLHpfafG5SsZlaHd2$. You are receiving this because you authored the thread.Message ID: @.***>