hiPathia

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====== 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. 

**The web version of Hipathia is limited to a maximum of 500 samples per dataset. For bigger datasets please use [[http://bioconductor.org/packages/release/bioc/html/hipathia.html|the R Bioconductor Hipathia package]]**