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bioinformatics-core-shared-training / Bulk_RNAseq_Course_Base

https://bioinformatics-core-shared-training.github.io/Bulk_RNAseq_Course_Base/
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Reference group "MUT" #19

Closed joowkim closed 1 year ago

joowkim commented 1 year ago

Hello,

It seems to me that the reference/baseline is "WT" instead of "MUT".

This is how the meta data is made. colData(dds) <- DataFrame(treatment = factor(rep(c("A", "B"), each = 6)), genotype = factor(rep(c("WT", "MUT"), 6), levels = c("WT", "MUT")), row.names = paste0("sample", 1:12))

The code here, The levels = c("WT, "MUT"), "WT" comes first, and model.matrix says something similar.

https://github.com/bioinformatics-core-shared-training/Bulk_RNAseq_Course_Base/blob/181df86fbe88d037ea3bcbf324fb98786f64bb1b/Markdowns/07_Linear_Models.Rmd#L962

tavareshugo commented 1 year ago

Many thanks for opening this issue @joowkim You were absolutely right, and we have fixed this now.