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--- data_format [2020/01/28 19:21] – krian
+++ data_format [2024/02/27 13:17] (current) – [Experimental design file format] krian
@@ Line 3: / Line 3: @@
 Different types of data are used in Hipathia. Some of this data require a certain structure explained on the following links:
+**Note:** The recommended file extensions are '.txt' or '.tsv'.
-[[Expression matrix file format |Expression matrix file format]]
+===== Expression matrix file format =====
-====== Headline ======
-===== Headline =====
-====== Headline ======
-======   - Ordered List Item ======
 Expression matrix file is a Tab-separated values file.
@@ Line 57: / Line 50: @@
 **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.
+<code>
+sample1	Group_1
+sample2	Group_1
+sample3	Group_2
+</code>
-[[Experimental design file format | Experimental design file format ]]
+**Note**: In case of **paired data** the Experimental design file must be **ordered**.
-[[Gene list file format | Gene list file format ]]
+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>
+====== Character encoding ======
+We recommend using the **[[https://en.wikipedia.org/wiki/UTF-8 | UTF-8]]** character encoding for your content or data.