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Diffstat (limited to 'topics/quality-control')
| -rw-r--r-- | topics/quality-control/qc-checks.gmi | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/topics/quality-control/qc-checks.gmi b/topics/quality-control/qc-checks.gmi new file mode 100644 index 0000000..55b4847 --- /dev/null +++ b/topics/quality-control/qc-checks.gmi @@ -0,0 +1,29 @@ +# Quality Control Checks + +1. Gene Symbols to ProbeSetId (Affymetrix format): + +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 8 decimal places. + +6. The average between male and female mice has to be computed. + +7. AVG values have to be computed to only 3 decimal places. + +8. Datasets/studies having the same ProbeSetID should be grouped together. + +9. There should be no trailing spaces in data cells. + +10. Entries should have the same capitalization style. |