Hi
Others can have better insight in your question so i tis preferable to post
your mails to the Rhelp list too.
I hope your datafile is all numeric. If not after t(datafile) can be character.
AFAIK your pvalue is not propagated to aov function.
Based on artificial data your construction arrives to result, which in this
case tells you that there is almost no difference in those 5 groups..
m <- data.frame(groups, data = rnorm(length(groups)))
> anova(aov(data ~ groups, m))
Analysis of Variance Table
Response: data
Df Sum Sq Mean Sq F value Pr(>F)
groups 4 9.20 2.2999 2.2117 0.06751 .
Residuals 326 338.99 1.0399
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
So I still wonder what is the problem. If you want to know whether
anova(aov(…)) is appropriate for your case you shall consult local statistician
or post your question e.g. on stackexchange or hope that somebody with deeper
statistical knowledge from R help subscribers can help you.
But you probably need to post some more info.
Cheers
Petr
From: hehsham alpukhity [mailto:hesham...@yahoo.com]
Sent: Tuesday, April 5, 2016 12:04 PM
To: PIKAL Petr <petr.pi...@precheza.cz>
Subject: Re: [R] use one way ANOVA to select genes
thanks Petr
Actually , i have wrote code for One way ANOVA ,but still i am sure is it true
or not for analysis data , because I have 5 groups i want to select the
significant gene from this groups , .
this code
#######################################################################################################
datafile <- read.csv("brcaResultsclust.csv",header = T,row.names = 1)
datafile <- t(datafile)
groups <- factor(rep(c("c1","c2","c3","c4","c5"),c(116,83,28,80,24))) # here
one factor with 5 groups
# define ANOVA function
aoftest <- function(data ,pvalue=0.05) {
m<-data.frame(groups, data);
anova(aov(data ~ groups, m))
}
anovaresultstest <- apply(datafile, 1, aoftest)
#############################################################################################
is the design factor and the function for ANOVA test is true ?
thank
hesham
On Monday, April 4, 2016 3:29 PM, PIKAL Petr
<petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> wrote:
Hi
Your message is scrambled by using HTML post and if I deciphered it correctly
you just want to use anova for some data.
What is preventing you from doing it?
Cheers
Petr
-----Original Message-----
From: R-help
[mailto:r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org>] On
Behalf Of hehsham alpukhity via R-help
Sent: Sunday, April 3, 2016 4:45 PM
To: R-help Mailing List <r-help@r-project.org<mailto:r-help@r-project.org>>
Subject: [R] use one way ANOVA to select genes
i want to select the significant genes form 5 clusters (groups) by one way
ANOVA in
r#######################################################################################
# i want use One way ANOVA to select the siginificant from the clusters above
selectgene <- function(GropuData,pvalue=0.05, na.rm=TRUE, file=1:5){# if each
gruop in one txt file fdata <- list.files(data,full.names =
TRUE) for(i in file) { anova()
} }######################################
Hisham AL-bukhaiti Ph.D Student (Information system ) China, changsha,Hunan
university. Mobile: 0068-15 111 4246 91.
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