## PuMaQC sample INI file a single search. ## 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 paths to files use either "\" or "/" - automatically corrected. ## File paths 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 combined, see IncludeX) ## List of include keywords to be searched. Logical "OR" is used for Include. ## ## Exclude: (single search, for combined, see ExcludeX) ## Optional list of exclude keywords. Logical "AND" is used for Exclude. ## ## 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 healthy lung microarrays [Search] GEOmetadb = ../GEOmetadb.sqlite Platform = HG-U133_Plus_2 Organism = Homo sapiens Include = lung, bronchus, respiratory Exclude = cancer, carcinoma, tumor, metasta, embryo, fetal Results = selectedGSM.txt [Import] DownloadTo = download CDF = N:/Data/_CDF/HG-U133_Plus_2.cdf APT = C:\APT-1.14.2\Bin Results = importedGSM.txt [QC] Alpha = 0.05 Annotate = TRUE Annotation = arrayQualityMetrics = TRUE Results = dataGoodQuality.txt