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Diffstat (limited to 'topics/quality-control')
-rw-r--r-- | topics/quality-control/qc-checks.gmi | 55 | ||||
-rw-r--r-- | topics/quality-control/qc.gmi | 41 | ||||
-rw-r--r-- | topics/quality-control/ui-design.gmi | 49 |
3 files changed, 0 insertions, 145 deletions
diff --git a/topics/quality-control/qc-checks.gmi b/topics/quality-control/qc-checks.gmi deleted file mode 100644 index dc18f94..0000000 --- a/topics/quality-control/qc-checks.gmi +++ /dev/null @@ -1,55 +0,0 @@ -# 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 deleted file mode 100644 index 7b5d1e4..0000000 --- a/topics/quality-control/qc.gmi +++ /dev/null @@ -1,41 +0,0 @@ -# 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 deleted file mode 100644 index 029a2b8..0000000 --- a/topics/quality-control/ui-design.gmi +++ /dev/null @@ -1,49 +0,0 @@ -# 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 |