[MRG] add a yeast differential expression example

dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system

https://dib-lab.github.io/elvers/

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[MRG] add a yeast differential expression example #108

Closed ctb closed 5 years ago

ctb commented 5 years ago

Fixes #109.

Adapted from my GGG class at UC Davis.

Two concerns --

[x] --build_config output no longer includes example contrasts (https://github.com/dib-lab/eelpond/issues/109#issuecomment-471198488)
[x] it looks to me like the MA plot might not be doing the right contrasts. I don't understand the relevant R code at the moment, so I can't be sure of what's going on...

ctb commented 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

ctb commented 5 years ago

it's working! I didn't understand samples.tsv; fixed in 3f753a1.

ctb commented 5 years ago

here are the updated PDFs -- they're beaaaaautiful! yeast_input.deseq2.pca.pdf yeast_input.cwt-vs-mut.deseq2.ma-plot.pdf

ctb commented 5 years ago

Ready for review & commentary @bluegenes

ctb commented 5 years ago

(awesome - the CI can run the yeast workflow too!)

ctb commented 5 years ago

fixed the deseq2 contrasts issue with #93!

@bluegenes this is ready for review & merge!

ctb commented 5 years ago

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 :)