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babelomics_tags [2017/05/24 10:36] (current)
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 +====== Babelomics Reserved Words ======
 +
 +Apart from the expression data some **additional information** is needed depending on the kind of analysis you are doing. In general this complementary information does not relate directly to the genes but to the experimental conditions. For example the //class// of the samples you are analyzing or the //survival times// of each cell culture are characteristic to all genes within one array.
 +
 +Some **tags** are used by [[Babelomics]] data files to incorporate this additional information to that of the expression measurements. Those reserved words are:
 +
 +  * **#NAMES**: used to introduce the names of the arrays
 +
 +  * **#CLASS**: used to introduce class labels
 +
 +  * **#SERIES**: used to introduce series labels
 +
 +  * **#INDEPENDENT_VARIABLE**: used to introduce values of array covariates in the context of correlation analysis
 +
 +  * **#TIME_VARIABLE**: used to introduce survival times
 +
 +  * **#CENSORING_VARIABLE**: used to indicate censored observations in the context of survival analysis
 +
 +  * **#CONTIN**: used to introduce time or dosage values in the context of time/dosage course analysis
 +
 +There are **two ways** of introducing such additional information in [[Babelomics]] [[differential expression]] module. One of them is to use **additional files** containing rows with the labels or values relating to each array. These special lines would contain a firs reserved word followed by the information about the sample. As usual in [[Babelomics]]' these labels have to be separated by **tab** and the file has to end with **newline** or carriage return. Several labels can be introduced in the same file byusing different [[reserved words]]
 +
 +For example, if you are analyzing arrays of two classes you will use a class label file that will contain a line looking like this:
 +
 +       #CLASS classA classB classA classA classB classA
 +
 +In you are analyzing **time series** the syntax should be as follows:
 +
 +       #SERIES    treatmentA  treatmentA  treatmentA  treatmentB  treatmentB  treatmentB
 +       #CONTIN      time1       time2       time3       time1       time2       time3
 +
 +The **second** way of introducing information about the conditions is to **insert** those **special lines** at the begining of your expression data file. 
 +
 +An example of expression data file with a special line for class labels would be:
 +
 +      #CLASS classA classB classA classA classB classA
 +      gene1 10.23 9.98 10.41 10.55 10.65 9.69
 +      gene2 10.51 9.74 10.65 10.63 10.43 10.35
 +      gene3 9.89 10.02 9.89 11.03 10.21 10.77
 +      gene4 10.25 10.83 8.94 10.16 10.49 10.46
 +      gene... ... ... ... ... ... ...
 +
 +
 +
 +
 +
  
babelomics_tags.txt · Last modified: 2017/05/24 10:36 (external edit)
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