Question: Running ANOVA in R on 4 different groups
0
janainamace • 10 wrote:
Hello everyone
I'm starting to use R to analyze proteomic data. I have 4 different groups and I would like to compare differentially expressed proteins. I would like to apply a One-way ANOVA followed by a Tukey post hoc test.
My data is organized as follows:
Group.......... Protein 1.......... Protein 2 ......Protein3025
A
A
B
B
C
C
D
D
data <- read.delim("~/ANOVA Test/data.txt")
data$Group <- factor(data$Group, levels=c("A","B","C", "D"))
data$Group
> [1] A A B B C C D D
> Levels: A B C D
myformula <- " ~ Group"
for (i in 2:ncol(data))
{
formula <- paste(colnames(data)[i], myformula, sep="")
p <- summary(aov(as.formula(formula), data=data))[[1]][["Pr(>F)"]][1]
print(paste(formula, ": p=", p, sep=""))
}
>[1] "Q9C075 ~ Group: p=0.000525021327472293"
>[1] "Q6A162 ~ Group: p=0.000525021327472293"
>[1] "O76009 ~ Group: p=0.000525021327472293"
>[1] "P0DN37 ~ Group: p=0.000389600632838321"
>[1] "P0DN26 ~ Group: p=0.000389600632838321"
>[1] "F5H284 ~ Group: p=0.000389600632838321"
....
So far, I have this result, but I would like to know which proteins are regulated in all comparisons, that is, AB, AC, AD, BC, DC. Can someone help me? Is this approach correct?
Thanks in advance
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modified 10 months ago
by
Kevin Blighe ♦ 69k
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written
10 months ago by
janainamace • 10
