Bioinformatics GEO Data Analysis

Raw data were processed and normalized using the limma package (version 3.50.0; R Foundation for Statistical Computing, Vienna, Austria) in R (version 4.1.0) .

Probe-level data were converted to gene symbols, and batch effects were corrected using the ComBat algorithm (part of the sva package, version 3.42.0) . Differential expression analysis was performed between premalignant adenomas and carcinomas, applying a threshold of FDR <0.05 and an absolute log₂ fold change >0.585. This integrative analysis identified consistently DEGs common to both cohorts for subsequent investigation.