Program

Synopsis

#command line arguments in the following way
args[0]:pval_file, 
args[1]:affy_go_file, 
args[2]:Go_name_file, 
args[3]:ug_file, 
args[4]:destination_file, 
args[5]:method, 
args[6]:class_max_size, 
args[7]:class_min_size, 
args[8]:number of runs, 
args[9]:quantile, 
args[10]:p-value, 
args[11]:weightcheck

**notce: all "data files" and this "command line file" should be put under the directory ermineJ\src

examples:
1. java erminecmd age.welch.pvals.highexpression.forerminej.txt MG-U74Av2.go.txt goNames.txt MG-U74Av2.ug.txt output-quantile-log2.txt QUANTILE_METHOD 100 4 10000 50 0.001 true
2. java erminecmd age.welch.pvals.highexpression.forerminej.txt MG-U74Av2.go.txt goNames.txt MG-U74Av2.ug.txt output-mean-log3.txt MEAN_METHOD 100 4 10000 50 0.0001 true

For program introduction and methods detail, please click here.

Inputs

Dataset I
1. Pval File  -- one-way-anova-parsed.txt
2. Affy GO File -- HG-U95Av2.go.txt 
3. Go Biological Names File --  goName.txt
4. Unigene File -- HG-U95Av2.ug.txt

Dataset II
1. Pval File  -- armstrong-owaov.txt
2. Affy GO File -- HG-U95Av2.go.txt 
3. Go Biological Names File --  goName.txt
4. Unigene File -- HG-U95Av2.ug.txt

Dataset III
1. Pval File  -- age.welch.pvals.highexpression.forerminej.txt
2. Affy GO File -- MG-U74Av2.go.txt 
3. Go Biological Names File --  goName.txt
4. Unigene File -- MG-U74Av2.ug.txt

Dataset IV
1. Pval File  -- schinke-owaov.txt
2. Affy GO File -- MG-U74Av2.go.txt 
3. Go Biological Names File --  goName.txt
4. Unigene File -- MG-U74Av2.ug.txt

Outputs

• for Dataset I     txt file    excel file
• for Dataset II    txt file    excel file
• for Dataset III   txt file    excel file
• for Dataset IV   txt file    excel file

Dependencies

• None.

Problems/bugs

• None known.

Version history

References