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Use the word 'transform' more consistently on DESeq2 steps #249

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merged 5 commits into from
Oct 6, 2020

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cansavvy
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@cansavvy cansavvy commented Sep 29, 2020

Purpose:

Closes #220

Strategy

I looked through the RNA-seq examples and looked for the sections where we applied DESeq2 transformations. I then searched and replaced those sentences that only mentioned normalization to mention transformation and link to the 00-rnaseq.html transformation section for more info.

I also found one TODO for a link to the rna-seq clustering heatmap link that I fulfilled.

And then of course, I ran snakemake on the docker container for re-rendering.

Concerns/Questions for reviewers:

Should I drop the word normalize entirely from these sections (I have not because I think people are more familiar with that word, so I kept it but added "transformation). So now everything says normalize and transform.

@cansavvy cansavvy marked this pull request as ready for review September 29, 2020 17:36
@cansavvy cansavvy changed the title Use the word transform more consistently on DESeq2 steps Use the word 'transform' more consistently on DESeq2 steps Sep 29, 2020
@cansavvy cansavvy requested a review from cbethell September 30, 2020 17:43
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Looks good to me @cansavvy! Just one suggestion to propagate the wording to the comments in the code chunk, otherwise 🚀

03-rnaseq/dimension-reduction_rnaseq_01_pca.Rmd Outdated Show resolved Hide resolved
03-rnaseq/dimension-reduction_rnaseq_02_umap.Rmd Outdated Show resolved Hide resolved
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Seems fine!

@cansavvy cansavvy merged commit a0eb1e5 into master Oct 6, 2020
@cansavvy cansavvy deleted the cansavvy/normalize-wording branch October 6, 2020 20:37
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RNA-seq modules: Be more clear about normalization vs transformation when using DESeq2 functions
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