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refine.bio compendia instead; also change illustration
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jaclyn-taroni committed Sep 26, 2019
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Expand Up @@ -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

Expand All @@ -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.
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