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| author | Frederick Muriuki Muriithi | 2024-02-16 04:18:10 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-02-16 04:18:10 +0300 |
| commit | efa2f6f14f314022bec1ef2e34dfdb826e9bb001 (patch) | |
| tree | adaa14ab58b42889171d42c221dc5299a5b5c884 | |
| parent | 62d993246fc312794d07422ecd3e6b409c46a96e (diff) | |
| download | gn-gemtext-efa2f6f14f314022bec1ef2e34dfdb826e9bb001.tar.gz | |
Mark sub-issue as done. Add new sub-issue.
| -rw-r--r-- | issues/quality-control/qc-r-qtl2-bundles.gmi | 8 |
1 files changed, 5 insertions, 3 deletions
diff --git a/issues/quality-control/qc-r-qtl2-bundles.gmi b/issues/quality-control/qc-r-qtl2-bundles.gmi index d975890..9cc1452 100644 --- a/issues/quality-control/qc-r-qtl2-bundles.gmi +++ b/issues/quality-control/qc-r-qtl2-bundles.gmi @@ -36,7 +36,8 @@ The following "key" details the meanings of certain notations in this file: ### [ ] pheno File(s) -* [ ] Check for a minimal number of decimal places (three?) +* [x] Check for a minimal number of decimal places (three?) +* [ ] Check that the numbers are log2 normalised (See 'Check for log2-normalised Values' section below) * [ ] Verify that all listed samples/cases exist in the database, prior to attempting to parse the file and load data into the database * [ ] If listed samples/cases do not exist in database, verify they are all listed in the "geno" file(s) @@ -46,9 +47,10 @@ This is a proposed addition for our specific use-case. If the data in the pheno Has similar QC checks to those for the "pheno" file(s) above. The number of decimal places might vary, however. -## Questions Fred Has +## Check for log2-normalised Values -* Is there a way to detect whether data has been log2 normalised? GN requires that all data is log2 normalised. +* Check that none of the values are negative +* Check that the values do not exceed 20 -- This is probably wrong, e.g. `mth.log2(3472935867452934)=51.62507719292422` ## Resources |