search

hbctraining / DGE_workshop_salmon_online

https://hbctraining.github.io/DGE_workshop_salmon_online/
163 stars 75 forks source link

Bug Fixes #37

Closed Gammerdinger closed 10 months ago

Gammerdinger commented 1 year ago

1) Add apeglm install from Biocmanager to instructions

2) Ensembldb has a filter function now that can overwrite dplyr, so be sure to put dplyr:: in front of filter commands like on the "Summarizing results and extracting significant gene lists" page: Change:

sigOE <- res_tableOE_tb %>%
        filter(padj < padj.cutoff)

To:

sigOE <- res_tableOE_tb %>%
        dplyr::filter(padj < padj.cutoff)

And on Visualization Change:

norm_OEsig <- normalized_counts[,c(1:4,7:9)] %>% 
  filter(gene %in% sigOE$gene)

To:

norm_OEsig <- normalized_counts[,c(1:4,7:9)] %>% 
  dplyr::filter(gene %in% sigOE$gene)
Gammerdinger commented 1 year ago

Also axes swap on time course lesson in text.