NA's after DA-GLMM

[yghosheh]

Hello,

Thank you for the package. It is well written. I have a paired-design experiment with different times of visits. I am trying to get DA-GLMM to work on an experiment with a design formula. The code I am using is the following:

ei <- metadata(sce3)$experiment_info da_formula <- createFormula(ei, cols_fixed = c("Clinical_Benefit","Visit", "Dose"), cols_random = c("sample_id", "Donor")) contrst <- createContrast(c(0, 1, 0, 0, 0, 0, 0, 0, 0, 0)) da_res <- diffcyt(sce3, formula = da_formula, contrast = contrst, analysis_type = "DA", method_DA = "diffcyt-DA-GLMM", clustering_to_use = "meta20", verbose = TRUE)

A sample of the experiment metadata

sample_id Donor Visit Dose Clinical_Benefit Stain_Batch n_cells 58101-002_PBMC_C1_300 58101-002 C1 300 No 200229 5e+05 58101-002_PBMC_C2_300 58101-002 C2 300 No 200229 5e+05 58105-001_PBMC_C1_300 58105-001 C1 300 Yes 200229 5e+05 58105-001_PBMC_C2_300 58105-001 C2 300 Yes 200229 483611 58105-001_PBMC_C4_300 58105-001 C4 300 Yes 200229 451636 58105-003_PBMC_C1_600 58105-003 C1 600 No 200229 5e+05 58105-003_PBMC_C2_600 58105-003 C2 600 No 200229 5e+05 58106-001_PBMC_C1_300 58106-001 C1 300 Yes 200229 5e+05

The levels for each of the fixed effects are: Clinical_Benefit: No | Yes Visit: C1 | C2 | C4 Dose: 45 | 135 | 300 | 600 | 1200

The command runs fine but I am just getting NAs in the output.

Thank you for your help.

Best regards,

Yanal

[shanh1]

Hi there! Did you manage to resolve this issue? I am having the same problem.