diff options
| -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 |