Merge pull request #57 from bcbio/devel

fix example data
bcbio · Nov 14, 2024 · 8c7a25d · 8c7a25d
2 parents d4a969e + 59502c7
commit 8c7a25d
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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') %>%