# Fstat: Calculation of F statistic by gene given a linear model In SAGx: Statistical Analysis of the GeneChip

## Description

Calculates F statistic.

## Usage

 `1` ```Fstat(indata = M, formula1 = ~as.factor(g), formula0 = "mean", design1 = NULL, design0 = NULL, B = NULL) ```

## Arguments

 `indata` The data matrix `formula1` a formula descibing the alternative linear model `formula0` a formula describing the nullmodel. Use linear models syntax, except for one-way ANOVA ("mean") `design1` the alternaive design matrix. If not NULL it overrides the formula argument `design0` the null design matrix. If not NULL it overrides the formula argument `B` the number of bootstrap replicates

## Value

A list with the components

 `Fstat` the value of the F statistic `fnum` the numerator degrees of freedom `fdenom` the denominator degrees og freedom `design1` the alternative design matrix `design0` the null design matrix `SS1` the sum of squares in the denominator of the F-statistic `SS0` the sum of squares in the numerator of the F-statistic `pvalue` the p-value for testing the alternative vs the null model

Per Broberg

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60``` ```## Annette Dobson (1990) "An Introduction to Generalized Linear Models". ## Page 9: Plant Weight Data. ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group <- gl(2,10,20, labels=c("Ctl","Trt")) weight <- c(ctl, trt) anova(lm.D9 <- lm(weight ~ group)) # Analysis of Variance Table # Response: weight # Df Sum Sq Mean Sq F value Pr(>F) #group 1 0.6882 0.6882 1.4191 0.249 #Residuals 18 8.7292 0.4850 Fstat(indata = rbind(weight,weight),formula1=~group) # Fstat will need at least two genes to work with # #\$Fstat # weight weight #1.419101 1.419101 #\$fnum # 18 #\$fdenom # 1 #\$design1 # (Intercept) groupTrt #1 1 0 #2 1 0 #3 1 0 #4 1 0 #5 1 0 #6 1 0 #7 1 0 #8 1 0 #9 1 0 #10 1 0 #11 1 1 #12 1 1 #13 1 1 #14 1 1 #15 1 1 #16 1 1 #17 1 1 #18 1 1 #19 1 1 #20 1 1 #attr(,"assign") # 0 1 # \$design0 # NULL # \$SS1 # weight weight #8.72925 8.72925 #\$SS0 # weight weight #0.688205 0.688205 ```

SAGx documentation built on Nov. 8, 2020, 8:18 p.m.