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Full-Text Articles in Genetic Structures
Systematic Evaluation Of Batch Effects In The Cancer Genome Atlas Program Underscores The Need For Batch-Controlled Analysis, Zhongxuan Chen, Stepan Nersisyan, Isidore Rigoutsos, Eric Londin
Systematic Evaluation Of Batch Effects In The Cancer Genome Atlas Program Underscores The Need For Batch-Controlled Analysis, Zhongxuan Chen, Stepan Nersisyan, Isidore Rigoutsos, Eric Londin
Alpha Omega Alpha Research Symposium Posters
Purpose: To systematically assess the impact of batch effects on differential expression of isomiR, mRNA, and non-coding RNA (sncRNA) across 13 The Cancer Genome Atlas (TCGA) cancer types and develop a standardized, batch-controlled analysis protocol for TCGA datasets.
Methods: Data analysis and visualization were performed using Python v3.12. Plots were generated using matplotlib and seaborn. isomiR, mRNA, and sncRNA sequences across 13 TCGA cancer types were used. Principal Component Analysis (PCA) was performed using scikit-learn for dimensionality reduction. Differential expression was conducted using DESeq2 under the following protocols: 1) primary tumor samples vs matched normal samples processed in the same …