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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:
 \\ \\
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       * 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//​__\\
pcamasigpro.txt · Last modified: 2014/05/12 12:42 by jcarbonell
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