ERROR:unused arguments (two.stage = TRUE, norm.option = "all", rescale = "residSD")

[uw-gac]

ERROR:unused arguments (two.stage = TRUE, norm.option = "all", rescale = "residSD")

[smgogarten]

You are likely using an older version of GENESIS from before these options were added. You can find your version with

library(GENESIS)
sessionInfo()

Bioconductor versions are linked to R versions, so first update your R installation to the most recent version, then follow the Bioconductor installation instructions to install the latest version of GENESIS.

[DamienTan]

Thanks for your reply! I have already installed GENESIS_2.29.0 from github before I submitted this issue.

> library(GENESIS)
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GENESIS_2.29.0

loaded via a namespace (and not attached):
 [1] quantsmooth_1.56.0     Rcpp_1.0.10            lattice_0.20-45        tidyr_1.2.1            Biostrings_2.58.0     
 [6] formula.tools_1.7.1    zoo_1.8-11             assertthat_0.2.1       lmtest_0.9-40          utf8_1.2.2            
[11] R6_2.5.1               GenomeInfoDb_1.26.7    backports_1.4.1        MatrixModels_0.5-1     gdsfmt_1.26.1         
[16] stats4_4.0.5           RSQLite_2.3.0          pillar_1.8.1           zlibbioc_1.36.0        rlang_1.0.6           
[21] rstudioapi_0.14        data.table_1.14.8      SparseM_1.81           blob_1.2.3             S4Vectors_0.28.1      
[26] Matrix_1.5-1           splines_4.0.5          BiocParallel_1.24.1    GWASExactHW_1.01       RCurl_1.98-1.10       
[31] bit_4.0.4              broom_1.0.1            compiler_4.0.5         pkgconfig_2.0.3        BiocGenerics_0.36.1   
[36] mgcv_1.8-40            tidyselect_1.2.0       GenomeInfoDbData_1.2.4 tibble_3.1.8           DNAcopy_1.64.0        
[41] IRanges_2.24.1         fansi_1.0.3            crayon_1.5.2           dplyr_1.0.10           MASS_7.3-58.1         
[46] bitops_1.0-7           grid_4.0.5             nlme_3.1-159           lifecycle_1.0.3        DBI_1.1.3             
[51] magrittr_2.0.3         SeqVarTools_1.28.1     cli_3.6.0              cachem_1.0.6           XVector_0.30.0        
[56] SNPRelate_1.24.0       mice_3.15.0            generics_0.1.3         vctrs_0.5.2            sandwich_3.0-2        
[61] tools_4.0.5            bit64_4.0.5            Biobase_2.50.0         glue_1.6.2             purrr_0.3.4           
[66] parallel_4.0.5         fastmap_1.1.0          survival_3.4-0         SeqArray_1.30.0        GenomicRanges_1.42.0  
[71] GWASTools_1.36.0       operator.tools_1.6.3   memoise_2.0.1          logistf_1.24.1         quantreg_5.94         

I restarted R just now. Maybe a older version was still loaded in the environment even though I installed the newest version. Glad to fix out this problem after restarting R.