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formats [2010/05/04 23:08]
aconesa
formats [2011/08/31 09:51] (current)
aconesa
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 We next explain each data file in detail: We next explain each data file in detail:
 \\ \\
-  ​ + \\ 
- * **Expression data**: txt file with expression data, genes in rows, arrays in columns. The file must contain an additional row with sample names and a column with gene names: \\ +  * **Expression data**: txt file with expression data, genes in rows, arrays in columns. The file must contain an additional row with sample names and a column with gene names. Column names should **not start with a number** and should also not contain strange characters\\ 
-|gene_names|sample_1|sample_2|sample_3|sample_4|sample_5|sample_6|sample_7|sample_8|sample_9+\\ 
-|gene_1|0.18|0.53|0.43|-0.99|-2.45|-1.18|1.43|2.32|0.32| +|Name|Array1|Array2|Array3|Array4|Array5|Array6|Array7|Array8|Array9|…
-|gene_2|1.22|0.91|1.52|1.23|-0.33|1.58|-2.31|-1.27|-1.08+|gene1|0.5|0.2|0.7|1.3|1.4|1.0|2.1|2.4|2.6|…| 
 +|gene2|0.5|0.3|0.4|0.3|0.4|0.1|0.1|0.4|0.5|…| 
 +|...|...|...|...|...|...|...|...|...|...|…
 +\\
   * **Covariates**:​ txt file with experimental design information,​ containing as many columns as arrays and as many rows as experimental factors. Each cell contains the value of the array in the experimental factor: \\   * **Covariates**:​ txt file with experimental design information,​ containing as many columns as arrays and as many rows as experimental factors. Each cell contains the value of the array in the experimental factor: \\
 + \\
 |Time|3|3|3|9|9|9|27|27|27|…| |Time|3|3|3|9|9|9|27|27|27|…|
 |Treatment|Ctr|TrA|TrB|Ctr|TrA|TrB|Ctr|TrA|TrB|…| |Treatment|Ctr|TrA|TrB|Ctr|TrA|TrB|Ctr|TrA|TrB|…|
- 
-   ​*//​Data//:​ txt file with expression data, genes in rows, arrays in columns. The file must contain an additional row with arrays names and a column with gene names. \\ 
-   ​*//​Covariates//:​ txt file with experimental design information,​ containing as many columns as arrays and as many rows as experimental factors. Each cell contains the value of the array in the experimental factor. E.g: 
 \\ \\
-|Time|3|3|3|9|9|9|27|27|27|+Experimental factors must have always **more than one level**, i.e. two or more time-points,​ two or more treatments, etc. If not, the experimental factor cannot be considered as such and should not be included in the covariates file. 
-|Treatment|Ctr|TrA|TrB|Ctr|TrA|TrB|Ctr|TrA|TrB|…+\\ 
- +\\ 
-   *//​Covariates//:​ txt file with experimental design informationcontaining as many columns as arrays and as many rows as experimental factors. Each cell contains ​the value of the array in the experimental factor. E.g:+  * **Annotation**:​ txt file with functional annotation of genes. Two columns: gene_annotation. If a gene has more than one annotation label, this is indicated in different rows: 
 + \\ 
 +|gene_1|GO:0005647| 
 +|gene_1|GO:0097635| 
 +|gene_2|GO:0000055| 
 +|gene_3|GO:0087630
 +|gene_3|GO:0008977| 
 +|...|...
 +\\ 
 +For data file examplesgo to the [[examples| Worked Examples]] Menu
 \\ \\
-|Time|3|3|3|9|9|9|27|27|27|…| 
-|Treatment|Ctr|TrA|TrB|Ctr|TrA|TrB|Ctr|TrA|TrB|…| 
formats.1273007285.txt.gz · Last modified: 2010/05/04 23:08 by aconesa
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