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libhts/libhts.py

@@ -105,10 +105,14 @@ def do_deseq2(cond_names, conditions, counts_data,
 
 
 def median_ratio_to_pseudo_ref_size_factors(counts_data):
-    """Adapted from DESeq paper (doi:10.1186/gb-2010-11-10-r106)"""
+    """Adapted from DESeq paper (doi:10.1186/gb-2010-11-10-r106)
+    All libraries are used to define a pseudo-reference, which has
+    the geometric mean across libraries for a given gene in *counts_data*.
+    For a given library, the median across genes of the ratios to the
+    pseudo-reference is used as size factor."""
     # Add pseudo-count to compute the geometric mean, then remove it
     #pseudo_ref = (counts_data + 1).apply(gmean, axis=1) - 1
-    # Ignore lines with zeroes instead:
+    # Ignore lines with zeroes instead (may be bad for IP: many zeroes expected):
     pseudo_ref = (counts_data[counts_data.prod(axis=1) > 0]).apply(gmean, axis=1)
     def median_ratio_to_pseudo_ref(col):
         return (col / pseudo_ref).median()