[[pcamasigpro]]
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pcamasigpro [2010/03/12 16:49] mjnueda |
pcamasigpro [2010/05/04 23:26] aconesa |
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| __Parameters for //PCA-maSigFun gene selection//__: | __Parameters for //PCA-maSigFun gene selection//__: | ||
| *//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.\\ | ||
| + | \\ | ||
| + | |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. E.g: | *//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: | ||
| \\ | \\ | ||
| Line 21: | Line 27: | ||
| * Proportion of acumulated variability. Posible cut-off values are in (0,1). | * Proportion of acumulated variability. Posible cut-off values are in (0,1). | ||
| * Proportion of variability of each PC. Posible cut-off values are in (0,1). | * Proportion of variability of each PC. Posible cut-off values are in (0,1). | ||
| - | * Average: components are selected that explain more than "cut-off" times the average component variability. The recommenden "cut-off" values are in [1,1.5]. | + | * Average: components are selected that explain more than "cut-off" times the average component variability. The recommended "cut-off" values are in [1,1.5]. |
| \\ | \\ | ||
| __Parameters for //PCA-maSigFun visualization//__\\ | __Parameters for //PCA-maSigFun visualization//__\\ | ||
