- R (packages: edgeR)
- Python (packages: pandas)
Rscript step0_preprocess.R
Rscript step1_calculateStats.R RNASeq
Rscript step1_calculateStats.R microarray
Rscript step2_findRef.R RNASeq
Rscript step2_findRef.R microarray
Since the example dataset has 115 samples in group1.
Rscript step3_overlapFisher.R 115 RNASeq
Rscript step3_overlapFisher.R 115 microarray
Rscript DDR_Ref.R
If you have another python version that has pandas:
Rscript DDR_Ref.R PYTHON_PATH
- final_out.csv: Normalized count data
- ref_cpm.csv: Expression of reference genes
- overlap_test_fdr_1_RNASeq.csv".csv: Differentially expressed genes with fdr < 0.1
- overlap_test_fdr_05_RNASeq.csv: Differentially expressed genes with fdr < 0.05