Rescue quality control issues from topics.

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diff --git a/topics/quality-control/qc-checks.gmi b/topics/quality-control/qc-checks.gmi
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-# Quality Control Checks
-
-1. ProbeSetId (Affymetrix format):
-
-We favour using Illumina, Affimetrix, and other platform formats.
-
-Custom formats require a new annotation file to be created.
-
-We usually use Ensemble ID or Gene IDs.
-
-1.1 Ensemble transcript IDs usually have duplicates that need to be pruned.
-
-ENSMBL1234
-
-## Example Gene Symbol to ProbeSetId
-
-AFFX-BkGr-GC03_st -> TCO500002136.mm.2
-
-2. Inbred Strain names should prefer long form:
-
-B6 -> C57BL/6
-D2 -> DBA/2
-
-3. Probeset IDs that don't have any values should be pruned:
-
-For example an Affymetrix data set might have ~28,000 entries and the data set that
-is allowed into the GeneNetwork will be 22,000 entries.
-
-4. The standard error between male and female mice has to be computed.
-
-5. SE values have to be computed to 6 or greater decimal places.
-
-6. The average between male and female mice has to be computed to 3 decimal places.
-
-7. Datasets/studies having the same ProbeSetID should be grouped together.
-
-8. There should be no trailing spaces in data cells.
-
-9. Entries should have the same capitalization style.
-
-10. Assesing Phenotypes for normality with Shapiro-Wilk Test.
-
-11. Check for annotations file.
-
-12. Check for CRLF.
-
-13. Check for UTF-8 encoding.
-
-## Tags
-
-* assigned: jgart
-* type: feature-request
-* priority: high
-* status: unclear
-* keywords: quality control
diff --git a/topics/quality-control/qc.gmi b/topics/quality-control/qc.gmi
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-# Quality Control Project
-
-Develop an app with a web interface to automate the job of cleaning tsv data
-files for entry. The app would be used by a group of users on a network to
-upload data.
-
-QC should be embedded functionality of the data uploader that Bonface has written.
-
-* Upload data through REST API - it goes into a temp dir for a user (data is in
-   escrow) - Bonface wrote this already
-* Run QC - what Arthur proposes (start here)
-* Show results - run tools (hard part!)
-* User can say - please accept data (Bonface wrote this)
-* Curator accepts data (different person!) (Bonface wrote this)
-* Data gets piped into GN proper
-
-The QC step consists of
-
-* Standard checks - some GN tools, such as outliers
-* Run mapping
-
-So, even though the data is in 'escrow' we should be able to use it as
-something that is in the database. GN1 does some of that. This is
-where Arun comes in - we need to have a common handler for data that
-is in the database and data that is in escrow. My idea is that this
-will all be text files (truth files). A simple first QC step is to
-check that all fields in the table are numbers where should be. Not
-text.
-
-Note we could run QC through the REST API too. That would allow it to
-be run from R and Python and Jupyter notebooks. Make it part of GN3.
-
-The tricky part is still how the data is handled in escrow.
-
-## Tags
-
-* assigned: jgart
-* priority: high
-* type: feature-request
-* status: in progress, beta
-* keywords: quality control
diff --git a/topics/quality-control/ui-design.gmi b/topics/quality-control/ui-design.gmi
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-# UI Design
-
-1. Input/Receive Data in UI (drag and drop/upload submit form)
-
-2. Select Mouse
-
-"What type of Group are you using?" 
-
-> (AKXD, BXH, Mouse Diversity Panel, BXD)
-
-3. "What is your platform?"
-
-> (Aff, Ilumina, ...)
-
-If Affymetrix (Aff) is selected then there should be various options
-like Clarion S.
-
-If the platform you chose is not available:
-
-  Tell PI that they should solicit for their platform to be added to the list.
-  
-  They can contact us via email.
-
-4. Allow excel file upload?
-
-## More Example UI Interactions and Checks
-
-"If your dataset does not comply with GN then you can try uploading your
-dataset so that we can inspect it."
-
-"Your dataset has two erroneous entries: Gene Accession Gene."
-
-"The last two columns have the wrong format for the strain name."
-
-"Here's our format of how your dataset should look like."
-
-> ProbeSetID Strains ...
-
-"Inbred Set ID 1 is the same as BXD"
-
-> These are the strains: ...
-
-## Tags
-
-* assigned: jgart
-* type: feature-request
-* status: unclear
-* priority: medium
-* keywords: UI, quality control