lpsymphony not returning a solution

[jmerkin]

Hello. I'm able to reproducibly run into this error with the a proprietary dataset (I work for a small biotech) that I unfortunately can't share, but I'll try to communicate and share what I can.

sym_get_col_solution(): No solution has been stored!
Error in if (all(ts == 0)) { : missing value where TRUE/FALSE needed
Calls: ihw_internal -> ihw_convex -> thresholds_to_weights

It looks like lpsymphony is having trouble. My guess is ts is all NA. Have you experienced this before or know what could cause it?

[jmerkin]

Actually, I can share the pvalues and weights.

I'm not doing anything crazy.

>ihwRes = ihw(pval ~ weight, data=table, alpha=.1, nbins=4)

returns
sym_get_col_solution(): No solution has been stored! Error in if (all(ts == 0)) { : missing value where TRUE/FALSE needed

>ihwRes = ihw(pval ~ weight, data=table, alpha=.1) (without specifying the number of bins)

raises the warning

sym_get_col_solution(): No solution has been stored!

but returns a result.

table.txt

`> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] readr_1.0.0 IHW_1.0.2 BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] tools_3.3.3 parallel_3.3.3 tibble_1.3.3
[4] Rcpp_0.12.11 slam_0.1-40 fdrtool_1.2.15
[7] BiocGenerics_0.18.0 rlang_0.1.1 lpsymphony_1.0.2`

[wolfganghuber]

Dear Jmerkin Thank you for your interest in this software, and for your feedback! Can I ask you to please post your question to https://support.bioconductor.org ? That way - other experts, who might even have better answers, get a chance to contribute - other users also benefit from the discussion - the question and answers are archived and remain findable in Google etc. Please also note posting guide: - use the most recent version of R (3.4.1.) and IHW from Bioconductor - share a MWE - post the required example data Kind regards Wolfgang 1.9.17 16:52, jmerkin scripsit:

…

Actually, I can share the pvalues and weights. I'm not doing anything crazy. |>ihwRes = ihw(pval ~ weight, data=table, alpha=.1, nbins=4)| returns |sym_get_col_solution(): No solution has been stored! Error in if (all(ts == 0)) { : missing value where TRUE/FALSE needed| |>ihwRes = ihw(pval ~ weight, data=table, alpha=.1)| (without specifying the number of bins) raises the warning |sym_get_col_solution(): No solution has been stored!| but returns a result. table.txt <https://github.com/nignatiadis/IHW/files/1270608/table.txt> `> sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] readr_1.0.0 IHW_1.0.2 BiocInstaller_1.22.3 loaded via a namespace (and not attached): [1] tools_3.3.3 parallel_3.3.3 tibble_1.3.3 [4] Rcpp_0.12.11 slam_0.1-40 fdrtool_1.2.15 [7] BiocGenerics_0.18.0 rlang_0.1.1 lpsymphony_1.0.2` — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE9STgVFlgr9Js1P_bKrkpqdarQfAlw1ks5seBo0gaJpZM4PKOvC>.

-- With thanks in advance- Wolfgang

------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany [email protected] http://www.huber.embl.de