Hi gabriel.hoffman ,

Thanks for developing the variancePartition package. I have been relying on it for a while with any analysis requiring mixed model.

Recently I realized that my previous results done a year ago are dramatically different with updated version. I had the exact same input and code, which was for a bulk ATAC experiment with 6 paired samples. Out of around 150k peaks, 8000 peaks had FDR<0.05 using version 1.28.5 while version >=1.33.11 had 0. I'm wondering if the changes in scaled weights that lead to this, and if so, what kind of situation is mostly affected by this update.

What would be your recommended version, considering the stable release on Bioconductor is still at 1.32.5.

Thanks! Le

  form <- ~Condition+(1|clone)+cov1+cov2
  param = SnowParam(6, "SOCK", progressbar=TRUE)

    edgeR::DGEList(count_matrix, group = covariates$Condition) -> edgeR_obj
    edgeR_obj$samples$lib.size<-sizeFactors
    scaleOffset(edgeR_obj,offset = cqn_edgeR) -> edgeR_obj
    vobjDream = voomWithDreamWeights(edgeR_obj, form, covariates, BPPARAM=param )
    gc()
    fitmmKR = dream( vobjDream, form, covariates, ddf="Kenward-Roger", BPPARAM=param)
    # fitmmKR = dream( vobjDream, form, covariates, BPPARAM=param)

    fitmmKR<-eBayes(fitmmKR)
    results_DREAM_KR<-topTable(fitmmKR,coef = 2 ,number = Inf) 


sessionInfo( )