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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