Closed ctb closed 5 years ago
The resulting PCA and MA plots are kinda wonky. Not sure if this is from filtering or from sample label wonkiness.
yeast_input.deseq2.pca.pdf yeast_input.cwt-vs-mut.deseq2.ma-plot.pdf
it's working! I didn't understand samples.tsv; fixed in 3f753a1.
here are the updated PDFs -- they're beaaaaautiful! yeast_input.deseq2.pca.pdf yeast_input.cwt-vs-mut.deseq2.ma-plot.pdf
Ready for review & commentary @bluegenes
(awesome - the CI can run the yeast workflow too!)
fixed the deseq2 contrasts issue with #93!
@bluegenes this is ready for review & merge!
On Tue, Mar 12, 2019 at 07:31:56PM +0000, Tessa Pierce wrote:
bluegenes commented on this pull request.
@@ -35,6 +35,8 @@ row.names(sample_info) <- sample_info$sample sample_info$sample <- NULL sample_info$condition <- factor(sample_info$condition)
+print(sample_info)
left in on purpose? @ctb
yes - turns out to be a very useful debugging step :)
Fixes #109.
Adapted from my GGG class at UC Davis.
Two concerns --
--build_config
output no longer includes example contrasts (https://github.com/dib-lab/eelpond/issues/109#issuecomment-471198488)