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formats [2010/05/04 23:16]
aconesa
formats [2011/08/31 09:51] (current)
aconesa
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-  * **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: \\
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-|gene_names|sample_1|sample_2|sample_3|sample_4|sample_5|sample_6|sample_7|sample_8|sample_9+|Name|Array1|Array2|Array3|Array4|Array5|Array6|Array7|Array8|Array9|…
-|gene_1|0.18|0.53|0.43|-0.99|-2.45|-1.18|1.43|2.32|0.32| +|gene1|0.5|0.2|0.7|1.3|1.4|1.0|2.1|2.4|2.6|…| 
-|gene_2|1.22|0.91|1.52|1.23|-0.33|1.58|-2.31|-1.27|-1.08|+|gene2|0.5|0.3|0.4|0.3|0.4|0.1|0.1|0.4|0.5|…| 
 +|...|...|...|...|...|...|...|...|...|...|…|
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   * **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: \\
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-|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|…|
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-Experimental factors must have always more than one level, i.e. two or more time-points,​ two or more treatments. If not, the experimental factor cannot be considered as such and should not be included in the covariates file. +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.
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   * **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:   * **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:
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 |gene_3|GO:​0087630| |gene_3|GO:​0087630|
 |gene_3|GO:​0008977| |gene_3|GO:​0008977|
-|Treatment|Ctr|TrA|TrB|Ctr|TrA|TrB|Ctr|TrA|TrB|+|...|...| 
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 +For data file examples, go to the [[examplesWorked Examples]] Menu
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formats.1273007781.txt.gz · Last modified: 2010/05/04 23:16 by aconesa
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