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scheidec wants to merge 10 commits into from
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Add median normalization functionality #1

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28dcfa9
Add medianNormalize() function
scheidec Nov 4, 2025
49ef92c
Enhance medianNormalize() with comprehensive validation
scheidec Jan 13, 2026
8b5be65
Streamline unit tests for medianNormalize()
scheidec Jan 13, 2026
071f956
Update medianNormalize function documentation
alexatSL Jan 28, 2026
8e47546
Simplify API, use sample-only defaults, add reverse ANML support
scheidec Feb 9, 2026
959a723
Remove sample selection parameters, use study samples only
scheidec Feb 9, 2026
7e2c445
Export reverseMedianNormalize() function
scheidec Feb 26, 2026
7be8264
update medianNormalize function documentation
alexatSL Mar 12, 2026
0fd12b6
Minor medianNormalize msg and documentation edits
scheidec Mar 16, 2026
346fb56
Add more robust checks to medNorm functions
scheidec Mar 16, 2026
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2 changes: 2 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -112,6 +112,7 @@ export(lift_adat)
export(loadAdatsAsList)
export(locateSeqId)
export(matchSeqIds)
export(medianNormalize)
export(meltExpressionSet)
export(merge_clin)
export(mutate)
Expand All @@ -123,6 +124,7 @@ export(read_adat)
export(read_annotations)
export(regexSeqId)
export(rename)
export(reverseMedianNormalize)
export(right_join)
export(rm_rn)
export(rn2col)
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14 changes: 13 additions & 1 deletion NEWS.md
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@@ -1,5 +1,17 @@
# SomaDataIO (6.5.0.9000)

### New Functions

* Added `medianNormalize()` function
- performs median normalization on `soma_adat` objects that have been
hybridization normalized and plate scaled
- includes validation to ensure required normalization steps have been applied
- supports multiple reference approaches:
- Internal reference built from study samples
- Reference extracted from existing `soma_adat` object
- External reference as a data.frame
- supports custom grouping by multiple clinical variables

### Function and Object Improvements

* Removed restrictive file validation from `read_annotations()`
Expand Down Expand Up @@ -35,7 +47,7 @@

* Updated `dplyr` verb tests to no longer explicitly test
for ordering of attributes (#165)

# SomaDataIO (6.4.0)

### New Functions
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