## PuMaQC sample INI file.
##  Use ";" or "#" characters to start comments. Sections are given in "[...]".
##  Parameters are followed by "=".  Keep all parameters. If you do not use one, 
##  simply remove the value after "=", e.g.
##      Exclude =
##  In the pathes to files use either "\" or "/" - automatically corrected.
##  File pathes can be given either relative to current INI file or absolute.  
##
##  See description below, followed by the meaningfull part of INI file.     
##==============================================================================
## [Project]
## Specify the project name and description (will be shown in the report) 
##==============================================================================
## [Search]
## In this section the parameters of the search are specified. 
##
## GEOmetadb:
## If you do not have GEOmetadb.sqlite, it will be automatically downloaded and 
## stored in the specified place. Better to use the same GEOmetadb.sqlite for 
## all your searched.  
## 
## Platform: 
## Put here either GPL (e.g. GPL570) of one of the following platform IDs:
##   HG-U133_Plus_2, HG-U133A_2, Mouse430_2, Rat230_2,
##   HuEx-1_0-st, MoEx-1_0-st, RaEx-1_0-st,
##   HuGene-1 0-st, MoGene-1_0-st, RaGene-1_0-st.
## Keep it empty for exploratory analysis of existing data.
## 
## Organism:
## Optional parameter, which is needed only for exploratory search
##
## Include:  (single search, for multple, see IncludeX) 
## List of include keywords to be searched. Logical "OR" is used for Include.  
##
## Exclude:  (single search, for multple, see ExcludeX) 
## Optional list of exclude keywords. Logical "AND" is used for Exclude.  
##
## IncludeX: (multiple search, for single, see Include) 
## List of include keywords to be searched in the query X. 
## X can be replaced by any name or number.   
##
## ExcludeX: (multiple search, for single, see Exclude) 
## Optional list of exclude keywords. Logical "AND" is used for Exclude.
##
## Expression: (multiple search, omit for a single search) 
## Combine results of several search unsing logical expression. Use AND, OR, NOT
## logical operators to uny, intersect or exclude the results. 
## Alternatively &,|,! can be used. Example: 
##   let Include1, Include2 and Include3 are specified.
##   then Expression = (1 OR 2) AND 3  will give intersection b/w 
##   search result 3 union of 1 and 2.
##
## Results:
## File with final search results. You can manually curate this file to exclude
## unwanted arrays.  
##==============================================================================
## [Import]
## DownloadTo: 
## The folder, where the downloaded CEL files will be stored.
## Note: it is not allowed to use path with SPACE here (APT restriction)
## 
## CDF:
## Path and name of corresponding CDF file. You can download CDF from 
## www.affymetrix.com  (after free registration).
## Note: it is not allowed to use path with SPACE here (APT restriction) 
##
## APT:
## Path to Affymetrix Power Tools (APT) executables. APT is accessible at 
## http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx
## 
## Results:
## File with the table of successfully downloaded and preprocessed data.
##==============================================================================
## [QC]
## Alpha:
## Quality Control threshold b/w 0 and 1, which is "alpha" parameter of a z-test. 
## The bigger value is given - more arrays are filtered out
## 
## Annotate:
## TRUE to annotate features (based on Affy annotation CSV file)
##
## Annotation:
## Affymetrix CSV file. If it is absent, it will be downloaded from 
## http://sablab.net/PuMaQC/lib (proper Platform alias should be given in Search section)
##
## arrayQualityMetrics:
## Assign "TRUE" to run in addition Kauffmann and Huber's pipeline.
##
## Results:
## Text file with the good quality results 
##==============================================================================


[Project]
Title = Lung project
Description = Look for lung from smokers with cancer and smokers without cancer

[Search]
GEOmetadb = ../GEOmetadb.sqlite
Platform = HG-U133_Plus_2
Organism = Homo sapiens

 # 1 - lung tissue
Include1 = lung
Exclude1 = metasta, embryo, fetal, cell line, tumor
 # 2 - smokers
Include2 = smoker, smoking
 # 3 - healthy
Include3 = healthy, normal
 # 4 - cancer
Include4 = cancer, carcinoma 

Expression = (1 and 2 and 3) or (1 and 2 and 4)
Results = selectedGSM.txt

[Import]
DownloadTo = download
CDF = ../../cdf/HG-U133_Plus_2.cdf
APT =C:\Program Files\Affymetrix Power Tools\APT-14.2\Bin 
Results = importedGSM.txt

[QC]
Alpha = 0.05
Annotate = TRUE
Annotation = 
arrayQualityMetrics = TRUE
Results = dataGoodQuality.txt