Kidney Transcriptomic Analysis — DEG Pipeline

Overview

Reproducible R pipeline for differential gene expression analysis of (Affymetrix Human Genome U133A Array), comparing renal tubular progenitor cells vs adult renal proximal tubule epithelial cells.

---

Dataset

Field	Value
GEO Accession
Platform	Affymetrix Human Genome U133A Array
Organism	Homo sapiens
Group 1	Renal tubular progenitor cells
Group 2	Adult renal proximal tubule epithelial cells

---

Pipeline Summary

┌─────────────────────────┐
│  1. Data Download       │  GEOquery → raw CEL files
├─────────────────────────┤
│  2. RMA Normalization   │  affy::rma() → expr_mat
├─────────────────────────┤
│  3. Quality Control     │  PCA, RLE, NUSE, MA plots
├─────────────────────────┤
│  4. Probe Annotation    │  hgu133a.db → Symbol, EntrezID
│     - Remove cross-hyb  │  (probes with "///" in Symbol)
│     - Remove no-symbol  │  (probes with NA mapping)
├─────────────────────────┤
│  5. DEG Analysis        │  limma + eBayes at probe level
│     - Threshold         │  |log2FC| > 1, raw P < 0.05
│     - FDR computed      │  BH adjustment (reported, not gated)
├─────────────────────────┤
│  6. Collapse to Genes   │  Best probe per gene (lowest P)
├─────────────────────────┤
│  7. Visualization       │  Volcano, MA, Scatter, Heatmap,
│                         │  Forest plot, Boxplots
└─────────────────────────┘