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ascagenes [2010/02/23 12:16]
mjnueda
ascagenes [2014/05/12 12:37] (current)
jcarbonell
Line 5: Line 5:
 __Parameters__:​ __Parameters__:​
    ​*//​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.\\    ​*//​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 factor. Each cell contains the value of the array in the experimental factor. ​E.g: +Example:​\\ 
-\\+|Name|Array1|Array2|Array3|Array4|Array5|Array6|Array7|Array8|Array9|…| 
 +|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 factor. Each cell contains the value of the array in the experimental factor.\\ 
 +Example:\\
 |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|…|
  
-   * //Join//: logical to indicate whether ​serial transcriptional changes ​should ​include time-zero non-null values ​(TRUE, default) or not (FALSE).\\ +   * //Include interaction between factors//: logical to indicate whether ​interaction/​s between factors ​should ​be analyzed ​(only for experimental designs with more than one factor).\\ 
-   * //Interaction//: logical to indicate whether ​interactions between factors should ​be analyzed.\\ +   * //Join interaction with second factor//: logical to indicate whether ​interaction/​s must be analysed jointly with the second/​third factor (TRUE, default) or not (FALSE).\\ 
-   * //​Variability//:​ average" ​to explain more than the average ​variation ​of the principal componentsA specific variation ​can be also indicated as 0.75 or 0.80...\\ +   * //​Variability ​threshold for component selection//: Criterion for selection of principal components. With "average"​, components are selected that explain more than the average ​component variability,​ calculated as total data variability divided by the rank of the matrix associated to the factorAlso a fixed value for percentage of explained variability ​can be indicated ​such as 0.2, 0.4, 0.5, 0.7, 0.8...\\ 
-   *//alpha//: significant level for gene selection.\\ +   * //Criterion for gene selection//. Strategy ​for selection ​of genes based on SPE and leverage valuesCan be either ​ 
-   ​*//R//: number ​of bootstrap rounds for gene selection.\\ +       ​* //Resampling//: where a null Leverage distribution is created by permuting columns ​of expression data and genes are selected at the "​alpha"​ percentile of the null distribution and SPE cutoff is computed by using an approximation to a weighted chi-squared distribution [[references|[2]]]
-  // +       * //minAS//: where a density function is calculated on the data and genes are selected on a local minimum basis [[references|[7]]]. 
- +       * //Gamma//: where a gamma distribution is adjusted to the distributions of SPE and leverage values, and genes are selected at the "​alpha"​ percentile of the gamma distribution [[references|[7]]].  
 +        
 +    
 +\\ 
ascagenes.1266923786.txt.gz · Last modified: 2010/02/23 12:16 by mjnueda
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