expression_matrix_file_format
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expression_matrix_file_format [2016/04/26 13:05] fsalavert created |
expression_matrix_file_format [2020/04/03 20:18] (current) |
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| ====== Expression matrix file format ====== | ====== Expression matrix file format ====== | ||
| - | Data matrix expression file is a Tab-separated values file. | + | 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...]] | 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...]] | ||
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| The first column corresponds to genes, probes or proteins, and the following IDs are accepted: | The first column corresponds to genes, probes or proteins, and the following IDs are accepted: | ||
| - | - Ensembl gene | + | * Ensembl gene |
| - | - HGNC symbol | + | * HGNC symbol |
| - | - Entrez id | + | * Entrez id |
| - | - Affy HG U133A probeset | + | * Affy HG U133A probeset |
| - | - Affy HG U133B probeset | + | * Affy HG U133B probeset |
| - | - Affy HG U133-PLUS-2 probeset | + | * Affy HG U133-PLUS-2 probeset |
| - | - Affy HTA 2.0 | + | * Affy HTA 2.0 |
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| </code> | </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. | ||
| - | You can download an usable example file from {{:brca_example1_40_exp.txt|here}} | + | **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]]** |
| - | + | ||
| - | **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. | + | |
expression_matrix_file_format.1461675922.txt.gz · Last modified: 2020/04/03 20:18 (external edit)
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