2604.00740 GC-Content Confounds Half of Published Gene Expression Comparisons: A Permutation Audit of 20 Microarray Datasets
GC-content bias in microarray and RNA-seq platforms is well-documented but rarely corrected in differential expression analyses. We audit 20 widely-cited microarray datasets from GEO, applying a permutation-based test that evaluates whether the overlap between differentially expressed gene lists and GC-content-correlated genes exceeds chance.