data_format
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data_format [2020/01/28 19:20] krian |
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| Different types of data are used in Hipathia. Some of this data require a certain structure explained on the following links: | Different types of data are used in Hipathia. Some of this data require a certain structure explained on the following links: | ||
| - | + | ===== Expression matrix file format ===== | |
| - | [[Expression matrix file format |Expression matrix file format]] | + | |
| - | + | ||
| - | ====== - Ordered List Item ====== | + | |
| Expression matrix file is a Tab-separated values file. | Expression matrix file is a Tab-separated values file. | ||
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| **Note**: If probe expression values are provided, these are recodified to gene expression values, obtained as the average value of all the probes mapping in the gene. | **Note**: If probe expression values are provided, these are recodified to gene expression values, obtained as the average value of all the probes mapping in the gene. | ||
| + | ===== Experimental design file format ===== | ||
| + | Experimental design is Tab-separated values file. This file has two columns, the first one corresponds to the sample name and the second one corresponds to the phenotype. | ||
| - | [[Experimental design file format | Experimental design file format ]] | ||
| - | [[Gene list file format | Gene list file format ]] | + | **Note**: In case of **paired data** the Experimental design file must be **ordered**. |
| + | |||
| + | Here is an example of a file with 4 piared samples (sample1_Normal and sample1_Treated are the same sample before and after treatment): | ||
| + | |||
| + | <code> | ||
| + | sample1_Normal Group_1 | ||
| + | sample2_Normal Group_1 | ||
| + | sample1_Treated Group_2 | ||
| + | sample2_Treated Group_2 | ||
| + | </code> | ||
| + | |||
| + | Here is an other file example see {{:brca_normal-basal_ed.txt|}}. | ||
| + | |||
| + | ===== Gene list file format ===== | ||
| + | |||
| + | Gene List is Tab-separated values file. This file has just one column, that is the Entrez ID of genes (1 Entrez ID per line). | ||
| + | |||
| + | |||
| + | Here is an example of a file with 4 genes to be evaluated: | ||
| + | |||
| + | <code> | ||
| + | Gene_1 | ||
| + | Gene_2 | ||
| + | Gene_3 | ||
| + | Gene_4 | ||
| + | </code> | ||
data_format.1580239232.txt.gz · Last modified: 2020/04/03 20:17 (external edit)
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