From 35c4cec2c3c1593b59bc29fa5a738f857ecc270f Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Tue, 19 Jul 2022 15:02:48 +0530
Subject: Rescue quality control issues from topics.

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 topics/quality-control/qc-checks.gmi | 55 ------------------------------------
 1 file changed, 55 deletions(-)
 delete mode 100644 topics/quality-control/qc-checks.gmi

(limited to 'topics/quality-control/qc-checks.gmi')

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
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