Commit 84272dc8 authored by Leon-Charles Tranchevent's avatar Leon-Charles Tranchevent
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Updated Limma procedure again with few more analyses and a small bug...

Updated Limma procedure again with few more analyses and a small bug correction (datasets without female patient).
parent 65f45819
......@@ -12,7 +12,7 @@ datasets:
- ['Simunovic', FALSE, 'HGU133A']
# We don't do that dataset since it has no gender mising and is the
# only one for that specific platform.
#- ['E-MEXP-1416', FALSE, 'XP3']
#- ['E-MEXP-1416', FALSE, 'U133_X3P']
- ['HG-U133A', TRUE, 'HGU133A']
- ['HG-U133_Plus_2', TRUE, 'HGU133Plus2']
......@@ -7,3 +7,5 @@ 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
test:
@Rscript --vanilla ${CODE_FOLDER}/get_DEGs.R GSE20141 > ${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).
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., female vs male, disease versus control).
This produces gene lists that can be used for pathway and network analyses.
# Details and instructions
......@@ -9,7 +9,10 @@ The 9 datasets and 2 meta-datasets are processed one by one to identify differen
- 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.
- Female patients vs male patients
- Female controls vs male controls
- (Female patients vs male patients) vs (Female controls vs male controls) [equivalent to #5]
Various plots and lists are created in the process. The results are summarized at the probe level but with gene annotations.
```
make clean_outputs
make run
......
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......@@ -2,14 +2,14 @@ local_input_data_dir: !!str '04/'
local_data_dir: !!str '05/'
local_code_dir: !!str '05-Get_DEGs/'
datasets:
- ['GSE20141']
- ['GSE20163']
- ['GSE20164']
- ['GSE20292']
- ['GSE7307']
- ['GSE7621']
- ['GSE8397']
- ['Simunovic']
- ['E-MEXP-1416']
- ['HG-U133A']
- ['HG-U133_Plus_2']
- ['GSE20141', 'HGU133Plus2', TRUE]
- ['GSE20163', 'HGU133A', TRUE]
- ['GSE20164', 'HGU133A', TRUE]
- ['GSE20292', 'HGU133A', TRUE]
- ['GSE7307', 'HGU133Plus2', FALSE]
- ['GSE7621', 'HGU133Plus2', TRUE]
- ['GSE8397', 'HGU133A', TRUE]
- ['Simunovic', 'HGU133A', TRUE]
- ['E-MEXP-1416', 'U133_X3P', TRUE]
- ['HG-U133A', 'HGU133A', TRUE]
- ['HG-U133_Plus_2', 'HGU133Plus2', TRUE]
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