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ascagenes [2010/02/28 16:10]
ascagenes [2014/05/12 12:37]
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 Example:\\ Example:\\
 |Name|Array1|Array2|Array3|Array4|Array5|Array6|Array7|Array8|Array9|…| |Name|Array1|Array2|Array3|Array4|Array5|Array6|Array7|Array8|Array9|…|
 |gene2|0.5|0.3|0.4|0.3|0.4|0.1|0.1|0.4|0.5|…| |gene2|0.5|0.3|0.4|0.3|0.4|0.1|0.1|0.4|0.5|…|
 |...|...|...|...|...|...|...|...|...|...|…| |...|...|...|...|...|...|...|...|...|...|…|
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 |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.txt · Last modified: 2014/05/12 12:37 by jcarbonell
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