====== Data format ======

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 is a Tab-separated values file.

A tab-separated values (TSV) file is a simple text format for storing data in a tabular structure (e.g. database or spreadsheet data). Each record in the table is one line of the text file. Each field value of a record is separated from the next by a tab stop character. [[https://en.wikipedia.org/wiki/Tab-separated_values|More about TSV...]]


This file has two columns if there is only one sample, and more than two columns if there are many samples.
The first line is a header and must contain the sample names. 
The first column corresponds to genes, probes or proteins, and the following IDs are accepted:

  * Ensembl gene
  * HGNC symbol
  * Entrez id
  * Affy HG U133A probeset
  * Affy HG U133B probeset
  * Affy HG U133-PLUS-2 probeset
  * Affy HTA 2.0


The next columns correspond to gene expression values in numeric format from each sample.

Here is an example of a file with only one example:

<code>
id	sampleName
1	0.3
2	1
3	0.73
</code>

And here is another example with more than one sample:

<code>
id	sample1	sample2	sample3
1	0.31	0.6	0.24
2	1	0.81	0.91
3	0.7	0.9	0.3
4	0.23	0.45	0.33
</code>

For a file example see {{:brca_genes_vals_bn.txt|}}

**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>

**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>
====== Character encoding ======
We recommend using the **[[https://en.wikipedia.org/wiki/UTF-8 | UTF-8]]** character encoding for your content or data.