I have a 2 factor experiment (2 mutations:A,B), with 2 levels (+/-) in each factor. All together there 4 conditions: wt, A, B, and A+B , with two replicates for each condition. I tried to use LRT test to isolate genes that are correspond to the mutations without interaction. the full model I used is ~A+B+A:B and the reduced is ~A:B I received the following error:
Error in nbinomLRT(object, full = full, reduced = reduced, quiet = quiet, : less than one degree of freedom, perhaps full and reduced models are not in the correct order
why are the degrees of freedom less than 1? Below I pasted the sessionInfo output. Thanks in advance.
R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362) Matrix products: default Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  grid parallel stats4 stats graphics grDevices  utils datasets methods base other attached packages:  ggplotify_0.0.5 gridExtra_2.3  dplyr_1.0.0 DESeq2_1.28.1  SummarizedExperiment_1.18.1 DelayedArray_0.14.0  matrixStats_0.56.0 Biobase_2.48.0  GenomicRanges_1.40.0 GenomeInfoDb_1.24.2  IRanges_2.22.2 S4Vectors_0.26.1  BiocGenerics_0.34.0 ggplot2_3.3.2  readxl_1.3.1 data.table_1.12.8 loaded via a namespace (and not attached):  Rcpp_126.96.36.199 locfit_1.5-9.4  lattice_0.20-41 assertthat_0.2.1  digest_0.6.25 R6_2.4.1  cellranger_1.1.0 RSQLite_2.2.0  pillar_1.4.4 zlibbioc_1.34.0  rlang_0.4.6 rstudioapi_0.11  annotate_1.66.0 blob_1.2.1  Matrix_1.2-18 labeling_0.3  splines_4.0.2 BiocParallel_1.22.0  geneplotter_1.66.0 pheatmap_1.0.12  RCurl_1.98-1.2 bit_1.1-15.2  munsell_0.5.0 compiler_4.0.2  pkgconfig_2.0.3 gridGraphics_0.5-0  tidyselect_1.1.0 tibble_3.0.1  GenomeInfoDbData_1.2.3 XML_3.99-0.4  fansi_0.4.1 crayon_1.3.4  withr_2.2.0 bitops_1.0-6  xtable_1.8-4 gtable_0.3.0  lifecycle_0.2.0 DBI_1.1.0  magrittr_1.5 scales_1.1.1  cli_2.0.2 farver_2.0.3  XVector_0.28.0 genefilter_1.70.0  ellipsis_0.3.1 rvcheck_0.1.8  generics_0.0.2 vctrs_0.3.1  RColorBrewer_1.1-2 tools_4.0.2  bit64_0.9-7 glue_1.4.1  purrr_0.3.4 survival_3.1-12  AnnotationDbi_1.50.1 colorspace_1.4-1  BiocManager_1.30.10 memoise_1.1.0