Example

This README will walk you through a simple usage of CLEP.

Alternatively run.sh can be executed to run the example for you

Downloading Data

1. Download the data, GSE65682
2. Unzip the file and and its constituent CEL files
3. Download and unzip the Platform Design file GPL13667-15572 and the MINIML xml file GSE65682_family.xml

Pre-Processing the Data

1. Add all the CEL filenames to a tab separated file with the heading as "FileName"

2. Run the preprocessing python script using the command,

   python3 preprocessing.py make-targets

3. Then process the expression matrix using the R affy_preprocessing script using the command,

   Rscript affy_preprocessing.R

4. Generate the expression file of the correct format using the python script,

   python3 preprocessing.py make-exp

Single Sample Scoring

• For limma based Single Sample Scoring, run,

  clepp preprocessing limma --data exp.txt --design targets.txt --out limma.txt

• For Z-Score based Single Sample Scoring, run,

  clepp preprocessing z-score --data exp.txt --design targets.txt --out z_score.txt