compareMetaDE

Integrative pipeline with metapro, customized metaDE(v.1.0.5) package and data generation steps for DE gene meta-analysis.

customized MetaDE package

Ordmeta and wFisher methods from metapro R package are integrated to MetaDE package to compare with. You can download metapro package here. Download: https://github.com/unistbig/metapro/
After metapro installation, you can install the the metapro package by typing open R and install the customized_MetaDE package by typing

install.packages(file.path(path_to_file,"MetaDE_1.0.5_customized_bukyung.tar.gz"), repos = NULL, type="source")

The original MetaDE package(v.1.0.5) is avaialable at CRAN. If you want to check, Download: https://cran.r-project.org/src/contrib/Archive/MetaDE/

📎 Dependency

check Dependencies before running main analysis.

• tidyverse
• magrittr

RNA-seq simulation

• Biobase
• edgeR
• limma
• SimSeq

meta analysis

• metapro
• MetaQC -install archived version, 0.1.13
• MetaDE -install customized package I uploaded

Visualization

• ggplot2
• reshape2
• ROCR
• colortools
• RColorBrewer
• VennDiagram

Simualation data analysis

simulation data generation

run simulation_data_generation.sh on shell.

./simulation_data_generation.sh 'working directory where rnaseq_voom_norm_simulation.R exists' 'output_directory'

Count and voom folders will be created after the run, data in the voom folder will be used for meta-analysis.

simulation data meta-analysis

run run_meta_simul.sh on shell.

./simulation_data_generation.sh 'working directory where Simulation_meta_analysis.R exists' 'input_directory where voom folder locate' 'output_directory'

Results will be saved in "output_directory/Meta_Res" folder.

Visualize simulation meta-analysis

run Visualize_simulation_meta_analysis.sh on shell.

./Visualize_simulation_meta_analysis.sh 'working directory where Visualize_simulation_meta_analysis.R exists' 'input_directory where voom folder locate' 'output_directory'

Plots will be saved in "output_directory/Simulation_analysis_plot" folder.

Microarray data analysis

True gene selection

run true_gene_selection.sh on shell.

./true_gene_selection.sh 'working directory where true_gene_selection.R exists' 'input_directory where prostate data locate' 'output_directory' 'true_de_gene_threshold'

Truegenes will be saved in output_directory. Other 6 study and 9 study analysis results will be saved in "output_directory/Meta_Res_real" folder. We used 0.01 of FDR threshold for true de gene selection.

real data simulation

run real_data_simulation.sh on shell

./real_data_simulation.sh 'working directory where real_data_simulation.R exists' 'input_directory where prostate data locate' 'output_directory' 'true_de_gene_threshold'

Results will be saved in "output_directory/Meta_Res_real" folder.

Visualize real data analysis

run Visualize_real_simulation_meta_analysis.sh on shell

./Visualize_real_simulation_meta_analysis.sh 'working directory where Visualize_real_simulation_meta_analysis.R exists' 'input_directory1 where real data simulation locate(Meta_Res_real folder we made)' 'input_directory2 where selected true genes locate' 'output_directory' 'true_de_gene_threshold'

Results will be saved in "output_directory/Real_study_analysis_plot" folder.