[R] use one way ANOVA to select genes

Tue Apr 5 12:45:29 CEST 2016

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:heshamibb at yahoo.com]
Sent: Tuesday, April 5, 2016 12:04 PM
To: PIKAL Petr <petr.pikal at 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.pikal at precheza.cz<mailto:petr.pikal at 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-bounces at r-project.org<mailto:r-help-bounces at 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 at r-project.org<mailto:r-help at 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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