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data_types [2010/05/30 23:35]
dmontaner created
data_types [2010/09/27 16:35] (current)
mbleda
Line 1: Line 1:
-[[Babelomics]] has internally defined [[data_types|data types]]. Each file you upload to [[Babelomics]] or you generate using the software is tagged with one or more reserved words identifying such //data types//.+===== Data Types =====
  
-[[data_types|Data types]] are useful ​to avoid computation mistakes and also to help you doing a meaningful analysis+[[Babelomics]] has internally defined data types. Each file you upload ​to [[Babelomics]] or you generate using the software is tagged with one or more reserved words identifying such //data types//.
  
-You cannot use all data files within all [[Babelomics]] tools. Only certain [[data_types|data ​types]] can be selected from within each tool, those for which the tool or method has been devised for.+Data types are useful to avoid computation mistakes and also to help you doing a meaningful analysis
  
 +You cannot use all data files within all [[Babelomics]] tools. Only certain data types can be selected from within each tool, those for which the tool or method has been devised for.
  
 +
 +Babelomics defines and uses different data type for internal usage and validation:
 +
 +   * **Microarray raw data**
 +   * **Expresion data matrix**
 +   * **ID lists**
 +   * **Newick format**
    
 +=== Expression data matrix ===
 +
 +Expression matrices are __numerical__ structures used to store expression data for **many** genomic **features** (genes, transcripts,​ exons...) form **several samples** (usually microarrays).
 +
 +Babelomics arranges **features in rows** and **samples in columns**.
 +
 +The first column of the matrix contains a name or **ID** for the genomic **feature** in each row. The first row of the file contains a name or **ID for the sample**. ​
 +
 +These values are usually stored in **tab delimited text files**; meaning that the columns of the file are separated by the TAB character.
 +
 +In the upper left top corner of the matrix the tag **#NAMES** is used by Babelomics to indicate that IDs are present in the matrix.
 +
 +In the firs rows of the file there may be some comment lines starting by **#**.
 +
 +An **example** of expression matrix file will look like this:
 +
 +;#;
 +{{images:​data_types_expression_matrix.png|Expression matrix}}
 +;#;
 + 
 +
 + 
 +
 +
  
data_types.txt ยท Last modified: 2010/09/27 16:35 by mbleda
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