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
Thank you so much Kevin! You helped me a lot.
Sure thing my friend / Valeu