Hello, I was wondering if there is a bug in the latest "edgeR" package as I get warning message after running estimateDisp function as below.
> v <- voom(y.norm, design = design, plot = T) > estDisp <- estimateDisp(y.norm, design, robust = T, weights = v$weights) Error in estimateDisp.default(y = y$counts, design = design, group = group, : formal argument "weights" matched by multiple actual arguments
Then, I tried, sample specific weights despite estimateDisp function clearly stats the weights argument is the numeric matrix of observation weight
> vq <- voomWithQualityWeights(y.norm, design = design, normalization = "none", plot = T) > estDisp_vqWts <- estimateDisp(y.norm, design, robust = T, weights = vq$targets$sample.weights) Error in estimateDisp.default(y = y$counts, design = design, group = group, : formal argument "weights" matched by multiple actual arguments
and got the same error.
I saw a recent reply here from Dr. Smyth that the bug has been fixed in the recent version but I thought mine would be due to a different reason.
Here is my session info and thank you very much for your time.
sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  rJava_0.9-11 dplyr_0.8.3 ggrepel_0.8.1 ggplot2_3.2.1 gplots_188.8.131.52 RColorBrewer_1.1-2  edgeR_3.26.8 Glimma_1.12.0 limma_3.40.6 BiocManager_1.30.4 XLConnect_0.2-15 XLConnectJars_0.2-15 loaded via a namespace (and not attached):  Rcpp_1.0.2 compiler_3.6.1 pillar_1.4.2 bitops_1.0-6 tools_3.6.1 digest_0.6.21 zeallot_0.1.0  statmod_1.4.32 jsonlite_1.6 tibble_2.1.3 gtable_0.3.0 lattice_0.20-38 pkgconfig_2.0.3 rlang_0.4.0  cli_1.1.0 rstudioapi_0.10 withr_2.1.2 vctrs_0.2.0 gtools_3.8.1 caTools_184.108.40.206 locfit_1.5-9.1  grid_3.6.1 tidyselect_0.2.5 glue_1.3.1 R6_2.4.0 fansi_0.4.0 gdata_2.18.0 purrr_0.3.2  magrittr_1.5 backports_1.1.4 scales_1.0.0 splines_3.6.1 assertthat_0.2.1 colorspace_1.4-1 labeling_0.3  utf8_1.1.4 KernSmooth_2.23-15 lazyeval_0.2.2 munsell_0.5.0 crayon_1.3.4