Issues

• GSL ERROR: matrix is singular in lu.c at line 449 errno 1

  genetics-statistics/GEMMA#306 · Filter by author huma-cloud opened on Jul 8, 2026
  1

• Input format for the -gxe option with paired measurements

  genetics-statistics/GEMMA#305 · Filter by author cedjf opened on Jun 26, 2026

• Question on GWAS validity when batch is completely confounded with phenotype

  genetics-statistics/GEMMA#302 · Filter by author C-YONG opened on Jan 28, 2026

• Discontinuous extreme p-values in GEMMA

  genetics-statistics/GEMMA#301 · Filter by author stephanie6688 opened on Jan 17, 2026

• How to get the residuals?

  genetics-statistics/GEMMA#300 · Filter by author moniquevdor opened on Oct 10, 2025

• Error with binary GWAS encoding

  genetics-statistics/GEMMA#298 · Filter by author hde08 opened on Aug 5, 2025

• can i use gemma lmm for very small samples (~n60)?

  notabug
  genetics-statistics/GEMMA#296 · Filter by author arkyl opened on Jun 6, 2025

• Support for K matrix with loading matrix Z

  genetics-statistics/GEMMA#292 · Filter by author lycium0605 opened on Feb 20, 2025

• Google group not accessible

  low priority
  genetics-statistics/GEMMA#291 · Filter by author hlnicholls opened on Feb 4, 2025
  3

• Extremely slow when conducting genome-wide multi-trait analysis

  genetics-statistics/GEMMA#288 · Filter by author ryshi06 opened on Dec 8, 2024

• macOS incompatibility

  Please help
  genetics-statistics/GEMMA#287 · Filter by author outpaddling opened on Dec 6, 2024
  1

• -gxe output

  genetics-statistics/GEMMA#286 · Filter by author liaguiro opened on Oct 4, 2024
  4

• random effects

  genetics-statistics/GEMMA#284 · Filter by author paolozambonelli opened on Aug 22, 2024

• ##ERROR: FAILED: Parsing input file 'mikk_small_hapVariants_updated_noheaders.csv' failed in function ReadFile_geno in src/gemma_io.cpp at line 744, for GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021

  genetics-statistics/GEMMA#282 · Filter by author fetche-lab opened on Jun 4, 2024
  4

• BIMBAM format (preferred)

  genetics-statistics/GEMMA#281 · Filter by author Sh1ne111 opened on Apr 4, 2024

• Identical P-Values at end of run

  genetics-statistics/GEMMA#280 · Filter by author jeremysutherland opened on Mar 21, 2024
  1

• ERROR: Enforce failed for Problem reading FAM file (phenotypes do not match geno file) in src/gemma_io.cpp at line 600 in ReadFile_fam GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020

  genetics-statistics/GEMMA#279 · Filter by author liuye2024 opened on Jan 3, 2024

• The problem of filtering snp parameters

  genetics-statistics/GEMMA#278 · Filter by author hhd1008611 opened on Dec 28, 2023
  6

• Why the diagonal of relatedness matrix is not equal to 1 or a constant value?

  genetics-statistics/GEMMA#277 · Filter by author xiekunwhy opened on Jun 26, 2023
  1

• WARNING: Brent did not converge

  genetics-statistics/GEMMA#276 · Filter by author MWQ1224 opened on May 31, 2023
  1

• GSL ERROR: function value is not finite in brent.c at line 58 errno 9

  genetics-statistics/GEMMA#275 · Filter by author zhoufc213 opened on Apr 20, 2023

• gsl: newton.c:88: ERROR: function value is not finite 3.08%

  genetics-statistics/GEMMA#274 · Filter by author jenny315 opened on Apr 19, 2023

• Got a nan in the p-value results

  genetics-statistics/GEMMA#273 · Filter by author voichek opened on Apr 11, 2023
  1

• gemma-wrapper:279:in `<main>': Expected GEMMA -a genotype file switch (RuntimeError)

  genetics-statistics/GEMMA#272 · Filter by author KizBaolin opened on Apr 2, 2023

• Pve is .999

  genetics-statistics/GEMMA#271 · Filter by author aguilar-gomez opened on Mar 31, 2023
  1