# Adjust\_batch() error **URL:** \ **Category:** MMUPHin\ **Created:** [April 5, 2021, 7:50pm UTC](https://forum.biobakery.org/t/adjust-batch-error/1892 "2021-04-05T19:50:22Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![Mary\_Swaney](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mary_swaney/32/530_2.png) [@Mary\_Swaney](https://forum.biobakery.org/u/Mary_Swaney)\ **Post date:** [April 5, 2021, 7:50pm UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/1 "2021-04-05T19:50:22Z")
Hello, I am trying to adjust for study effects between two microbiome studies and their abundance data using adjust\_batch(), but am receiving the following error: “Error in relocate\_scale(s\_data, l\_params\_shrink, batchmod, n\_batch, l\_ind) : Features determined to be eligible for batch estimation do not agree with the ones with valid per-batch shrinked parameters!”. I’m not sure exactly what this means or how to troubleshoot. If this helps, here is the verbose output: “feature\_abd is counts Found 2 batches Adjusting for covariate(s) or covariate(s) level(s) Pseudo count is not specified and set to half of minimal non-zero value: 5e-01 Adjusting for (after filtering) 6583 features Standardizing data across features Estimating batch difference parameters and EB priors Performing shrinkage adjustments on batch difference parameters Performing batch corrections Error in relocate\_scale(s\_data, l\_params\_shrink, batchmod, n\_batch, l\_ind) : Features determined to be eligible for batch estimation do not agree with the ones with valid per-batch shrinked parameters! In addition: Warning message: In check\_batch(df\_batch[[batch]], min\_n\_batch = 2) : Batch variable is not a factor as provided and will be converted to one.” Any guidance would be appreciated! Thank you -Mary ---
**Author:** ![sma](https://avatars.discourse-cdn.com/v4/letter/s/dec6dc/32.png) [@sma](https://forum.biobakery.org/u/sma)\ **Post date:** [April 6, 2021, 1:59am UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/2 "2021-04-06T01:59:22Z")
Hi - This is rare situation where something went gone wrong during estimating per-batch shifting and scaling parameters. Would you mind sharing your input data with me? You can reach me at [syma.research@gmail.com](mailto:syma.research@gmail.com). Thanks! Siyuan ---
**Author:** ![Mary\_Swaney](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mary_swaney/32/530_2.png) [@Mary\_Swaney](https://forum.biobakery.org/u/Mary_Swaney)\ **Post date:** [April 7, 2021, 3:43pm UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/3 "2021-04-07T15:43:52Z")
Hi Siyuan. Thanks for the response. I sent my input data to your email. Let me know if you need anything else! -Mary ---
**Author:** ![sma](https://avatars.discourse-cdn.com/v4/letter/s/dec6dc/32.png) [@sma](https://forum.biobakery.org/u/sma)\ **Post date:** [April 7, 2021, 9:04pm UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/4 "2021-04-07T21:04:12Z")
Hi Mary, Thanks for sending the data. It seems the error was caused by some rare cases where a feature has zero variance in non-zero values in a single batch. I’ve fixed this and pushed the change to Bioconductor. It’ll take a day or two for the new build to be sync’ed (the new version should be 1.4.2 instead of 1.4.1). Alternatively, you can install the fix directly from GitHub: `devtools::install_github("biobakery/MMUPHin")` Let me know if this solves the issue. Thanks, Siyuan ---
**Author:** ![Mary\_Swaney](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mary_swaney/32/530_2.png) [@Mary\_Swaney](https://forum.biobakery.org/u/Mary_Swaney)\ **Post date:** [April 8, 2021, 1:06am UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/5 "2021-04-08T01:06:15Z")
Hi Siyuan, It seems to be working now! Thank you again for the quick responses. I appreciate it. -Mary ---
**Author:** ![a\_foxx](https://avatars.discourse-cdn.com/v4/letter/a/a587f6/32.png) [@a\_foxx](https://forum.biobakery.org/u/a_foxx)\ **Post date:** [February 1, 2022, 6:22pm UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/6 "2022-02-01T18:22:34Z")
Hello, I am having the same issue with the error + warnings below using MMUPHin version 1.6.2: Error in relocate\_scale(s\_data, l\_params\_shrink, batchmod, n\_batch, l\_ind) : Features determined to be eligible for batch estimation do not agree with the ones with valid per-batch shrinked parameters! In addition: Warning messages: 1: In max(abs(g.new - g.old)/g.old, abs(d.new - d.old)/d.old, na.rm = TRUE) : no non-missing arguments to max; returning -Inf 2: In max(abs(g.new - g.old)/g.old, abs(d.new - d.old)/d.old, na.rm = TRUE) : no non-missing arguments to max; returning -Inf I’d greatly appreciate any further advice with this problem and would be happy to share more info on my data. AF ---
**Author:** ![sma](https://avatars.discourse-cdn.com/v4/letter/s/dec6dc/32.png) [@sma](https://forum.biobakery.org/u/sma)\ **Post date:** [February 1, 2022, 7:21pm UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/7 "2022-02-01T19:21:44Z")
Hi - Would you mind sharing the data? Feel free to email me at [syma.research@gmail.com](mailto:syma.research@gmail.com). Best, Siyuan ---
**Author:** ![sma](https://avatars.discourse-cdn.com/v4/letter/s/dec6dc/32.png) [@sma](https://forum.biobakery.org/u/sma)\ **Post date:** [February 6, 2022, 9:57pm UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/8 "2022-02-06T21:57:58Z")
To follow up: the issue has been fixed in GitHub MMUPHin 1.9.1. Update has been pushed to to Bioc release and should be available soon (version 1.8.1). ---
**Author:** ![SalmaES](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/salmaes/32/1113_2.png) [@SalmaES](https://forum.biobakery.org/u/SalmaES)\ **Post date:** [February 22, 2022, 8:03pm UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/9 "2022-02-22T20:03:52Z")
Hi Siyuan, I also seem to be getting the same error even after the update (I’ve pasted it below). I’m not sure what to, especially that I know I’ve got 4 batches. feature\_abd is counts Found 4 batches Adjusting for covariate(s) or covariate(s) level(s) Pseudo count is not specified and set to half of minimal non-zero value: 1e+00 Adjusting for (after filtering) 90 features Standardizing data across features Estimating batch difference parameters and EB priors Error in if (s2 == 0) s2 ← 1 : missing value where TRUE/FALSE needed In addition: Warning message: In check\_batch(df\_batch[[batch]], min\_n\_batch = 2) : Batch variable is not a factor as provided and will be converted to one. Thanks a lot! Salma ---
**Author:** ![sma](https://avatars.discourse-cdn.com/v4/letter/s/dec6dc/32.png) [@sma](https://forum.biobakery.org/u/sma)\ **Post date:** [February 24, 2022, 11:52pm UTC](https://forum.biobakery.org/t/adjust-batch-error/1892/10 "2022-02-24T23:52:08Z")
Hi - if you are comfortable, could you email me your data? Thanks, Siyuan [syma.research@gmail.com](mailto:syma.research@gmail.com)