diff --git a/inst/templates/rnaseq/DE/DEG.Rmd b/inst/templates/rnaseq/DE/DEG.Rmd index 9f02750..220d531 100644 --- a/inst/templates/rnaseq/DE/DEG.Rmd +++ b/inst/templates/rnaseq/DE/DEG.Rmd @@ -393,8 +393,8 @@ names(contrasts)=names_to_use de_list=lapply(contrasts, function(contrast){ resLFC = results(de, contrast=contrast) coef = paste0(contrast[1], "_", contrast[2], "_vs_", contrast[3]) - resLFCS <- lfcShrink(de, coef=coef, type="apeglm") - # resLFCS <- lfcShrink(de, contrast=contrast, type="ash") + # resLFCS <- lfcShrink(de, coef=coef, type="apeglm") + resLFCS <- lfcShrink(de, contrast=contrast, type="ash") res <- as.data.frame(resLFCS) %>% rownames_to_column('gene_id') %>% left_join(rdata, by = 'gene_id') %>%