Differential Gene Expression (DGE) Analysis in Microarray Data of Breast Cancer Subtypes
Objectives :
- Perform gene filtering to filter out less expressive genes.
- Give recommendations for genes that are expressed differently between four cancer subtypes: Luminal A, Luminal B, Basal, and HER.
- Investigate genes that are expressed differently between normal cell and cancer cell.
- Dataset: GSE45827 on breast cancer gene expression from Curated Microarray Database (CuMiDa);
- Platform: GPL 570
- Filtering:
genefilter
; - Gene Expression Analysis:
limma
,t-test
; - Gene Ontology:
GO.db
.
Dataset GSE45827 on breast cancer gene expression from CuMiDa
- 6 classes
- 54676 genes
- 151 samples
- Sampling
- Gene filtering
- Gene expression analysis: LIMMA (linear models for microarray data), t-test
- Gene ontology