Commit 65f45819 authored by Leon-Charles Tranchevent's avatar Leon-Charles Tranchevent
Browse files

Updated Limma procedure (added more analyses / restructured the code).

parent 8280449f
......@@ -5,7 +5,7 @@ This produces clean datasets that can be used for further analyses.
# Details and instructions
The 9 datasets are processed one by one to remove the bad arrays and update the clinical files accordingly. The clinical data is also updated to include gender predictions (from the local configuration file).
```
make cleanO
make clean_outputs
make run
```
The meta-datasets are already half-clean (because bad arrays can influence batch correction), so we perform the other half of the cleaning here (SCAN-no converg, QC-II and CLIN-no-gender). Please note that the 'Batch.tsv' file is not updated since it is not used after preprocessing with SCAN.
......
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/05/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/05-Get_DEGs/
clean:
@rm -rf *~
clean_outputs:
@rm -rf ${OUTPUT_FOLDER}/*
run:
@Rscript --vanilla ${CODE_FOLDER}/get_DEGs.R > ${OUTPUT_FOLDER}/run_log.out 2> ${OUTPUT_FOLDER}/run_log.err
# Objectives
The objectives of this step is to identify the differentially expressed genes of each dataset / meta-dataset, and for various comparisons of interest (e.g., fameale vs male, disease versus control).
This produces gene lists that can be used for pathway and network analyses.
# Details and instructions
The 9 datasets and 2 meta-datasets are processed one by one to identify differentially expressed genes (using limma). The following analyses are performed:
- Females vs males
- PD patients vs controls
- Female PD patients vs female controls
- Male PD patients vs male controls
- (Female PD patients vs female controls) vs (Male PD patients vs male controls)
Various Venn diagrams and gene lists are produceds in the process.
```
make clean_outputs
make run
```
# Prerequisites
The only prerequisite is to have the preprocessed and cleaned data for all datasets / meta-datasets (Step 04).
This diff is collapsed.
local_input_data_dir: !!str '02/'
local_input_data_dir: !!str '04/'
local_data_dir: !!str '05/'
local_code_dir: !!str '05-Get_DEGs/'
datasets:
......@@ -11,3 +11,5 @@ datasets:
- ['GSE8397']
- ['Simunovic']
- ['E-MEXP-1416']
- ['HG-U133A']
- ['HG-U133_Plus_2']
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