Add how baseline expression data is processed to documentation

AsierGonzalez commented 4 years ago

Currently the only information about baseline expression in the documentation is the list of the baseline sources in the target profile documentation and how the tissue specificity is calculated in the FAQs. We should find a new page with the information available in this Google doc.

andrewhercules commented 4 years ago

@AsierGonzalez is this ready or shall we push to the 20.09 release?

AsierGonzalez commented 4 years ago

I wrote the documentation and I am awaiting the feedback from @deniseOme and instructions as to where we should put it. From my end, I hope to have it ready for this release even if it's after the platform is out.

AsierGonzalez commented 4 years ago

The documentation is now available at https://docs.targetvalidation.org/getting-started/baseline-expression. I leave the ticket open for now as I would still appreciate if @deniseOme or @iandunham or someone else would like to share some feedback.

iandunham commented 4 years ago

This sentence is ambiguous "The tissue- and cell-based samples are processed together separately". Do you mean "The tissue- and cell-based samples are processed separately"?

iandunham commented 4 years ago

"assumed no to be" => "assumed not to be"

Otherwise this looks good. The language could be tightened up a bit - is there a version to edit for the future?

AsierGonzalez commented 4 years ago

Thank you for the feedback. I have corrected both mistakes in the Google doc, where you can add comments or make edits.

deniseOme commented 4 years ago

Following adjustments TODO:

include screenshots or a short animation if available to illustrate what we mean by Expression Atlas (EA) widget
make clear the normalisation and other steps are done by EA not by us
minor changes such as Gene Expression Atlas --> Expression Atlas (plus hyperlinking these resources)
mention RNA baseline data comes from both microarray and RNA sequencing experiments

We'd need to include the following as well:

details on how the Summary view is obtained (where mRNA and protein can be compared side by side)
GTEx variability plot: which file we have used? How did we compute/display the expression variance?

As it stands we are mainly talking about the Expression Atlas widget (in the tab in the target profile page). Is that the aim @AsierGonzalez? If so, no need to address the above 2 points (summary and GTEx plot).

@iandunham, we have the current text in this google doc page with links to Asier's original doc. Feel free to make changes to the text in there.

deniseOme commented 4 years ago

Clarification/confirmation from @AsierGonzalez : baseline expression data is available from RNA sequencing experiments only. No microarray data for baseline, only differential expression (not the subject of this help page).

deniseOme commented 4 years ago

Clarification 2 from @AsierGonzalez : this piece of documentation pertains only to the Summary tab; not to Expression Atlas or GTEx tabs under "RNA and protein baseline expression" section. We will make this clearer in the docs.

(current Platform)

(alpha release)

AsierGonzalez commented 4 years ago

@deniseOme is there anything left to do here?

opentargets / issues

Add how baseline expression data is processed to documentation #1011