From 1df6ac77066ed6c5ef1b8a0439e659bc21c57e90 Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni Date: Thu, 26 Sep 2019 10:41:05 -0400 Subject: [PATCH] refine.bio compendia instead; also change illustration --- docs/main_text.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/main_text.md b/docs/main_text.md index 412af92..67d4379 100644 --- a/docs/main_text.md +++ b/docs/main_text.md @@ -404,11 +404,11 @@ Specifically, the `aggregate_by` and `scale_by` fields note how the samples are The `quantile_normalized` fields notes whether or not quantile normalization was performed. Currently, we only support skipping quantile normalization for RNA-seq experiments when aggregating by experiment on the web interface. -# Species Compendia +# refine.bio Compendia We periodically release compendia comprised of all the samples from a species that we were able to process. -We refer to these as **species compendia**. -We offer two kinds of species compendia: [normalized compendia](#normalized-compendia) and [RNA-seq sample compendia](#rna-seq-sample-compendia). +We refer to these as **refine.bio compendia**. +We offer two kinds of refine.bio compendia: [normalized compendia](#normalized-compendia) and [RNA-seq sample compendia](#rna-seq-sample-compendia). ## Normalized compendia @@ -423,9 +423,9 @@ We use a full outer join because it allows us to retain more genes in a compendi ![outer join](https://user-images.githubusercontent.com/15315514/44534241-4dde9100-a6c5-11e8-8a9c-aa147e294e81.png) -We perform an outer join each time samples are combined in the process of building species compendia. +We perform an outer join each time samples are combined in the process of building normalized compendia. -![docs-species-compendia](https://user-images.githubusercontent.com/15315514/48498088-72995f00-e803-11e8-8832-3a9024748431.png) +![docs-normalized-compendia](https://user-images.githubusercontent.com/15315514/65698014-ddcdd780-e049-11e9-8ed6-f1d2f8ac2ee7.png) Samples from each technology—microarray and RNA-seq—are combined separately. In RNA-seq samples, we filter out genes with low total counts and then `log2(x + 1)` the data.