Set default to 1

DendrouLab · Mar 6, 2024 · 22c71e8 · 22c71e8
1 parent 5be421b
commit 22c71e8
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md
@@ -415,10 +415,10 @@ This can help to determine any inconsistencies in staining per channel and other
 
 ### Centered log ratio (CLR) normalization options
 
-<span class="parameter">clr_margin</span> `Integer`, Default: 0<br>
+<span class="parameter">clr_margin</span> `Integer`, Default: 1<br>
     Margin determines whether to normalize per cell (as you would do for RNA normalization), 
     or by feature (recommended, due to the variable nature of prot assays). 
-    CLR margin 0 is recommended for informative QC plots in this pipeline.
+    CLR margin 1 is recommended for informative QC plots in this pipeline.
   - 0 = normalise row-wise (per cell)
   - 1 = normalise column-wise (per feature, recommended)
 

diff --git a/panpipes/panpipes/pipeline_ingest/pipeline.yml b/panpipes/panpipes/pipeline_ingest/pipeline.yml
@@ -175,10 +175,10 @@ normalisation_methods: clr
 
 # margin determines whether you normalise per cell (as you would for RNA),
 # or by feature (recommended, due to the variable nature of prot assays).
-# CLR margin 0 is recommended for informative qc plots in this pipeline
+# CLR margin 1 is recommended for informative qc plots in this pipeline
 # 0 = normalise row-wise (per cell)
 # 1 = normalise column-wise (per feature, recommended)
-clr_margin: 0
+clr_margin: 1
 
 #--------------------------------------------------------------
 # Denoised and Scaled by Background (DSB) normalization options