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+ | ====== Babelomics Reserved Words ====== | ||
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+ | 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. | ||
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+ | Some **tags** are used by [[Babelomics]] data files to incorporate this additional information to that of the expression measurements. Those reserved words are: | ||
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+ | * **#NAMES**: used to introduce the names of the arrays | ||
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+ | * **#CLASS**: used to introduce class labels | ||
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+ | * **#SERIES**: used to introduce series labels | ||
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+ | * **#INDEPENDENT_VARIABLE**: used to introduce values of array covariates in the context of correlation analysis | ||
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+ | * **#TIME_VARIABLE**: used to introduce survival times | ||
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+ | * **#CENSORING_VARIABLE**: used to indicate censored observations in the context of survival analysis | ||
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+ | * **#CONTIN**: used to introduce time or dosage values in the context of time/dosage course analysis | ||
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+ | 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]] | ||
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+ | 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: | ||
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+ | #CLASS classA classB classA classA classB classA | ||
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+ | In you are analyzing **time series** the syntax should be as follows: | ||
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+ | #SERIES treatmentA treatmentA treatmentA treatmentB treatmentB treatmentB | ||
+ | #CONTIN time1 time2 time3 time1 time2 time3 | ||
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+ | The **second** way of introducing information about the conditions is to **insert** those **special lines** at the begining of your expression data file. | ||
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+ | An example of expression data file with a special line for class labels would be: | ||
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+ | #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... ... ... ... ... ... ... | ||
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