Re: [R] Calculating the t-test for each row

From: John Kane <jrkrideau_at_yahoo.ca>
Date: Mon, 03 Mar 2008 12:47:26 -0500 (EST)


If I understand you correctly what you want to do is do t-test (mu=0) for each column of the data.

Treating the data as a data.frame rather than a matrix you can do something like this and then pick out the p-values but with 140 t-tests I don't know what you'll get in terms of anything meaninful.


aa <- data.frame(a=rnorm(25, 5, 2), b=rnorm(1:25, 0,1))
mytea <- apply(aa, 2, t.test)

tresults <- lapply(mytea, function(.tres) {  

data.frame(t.value=.tres[1],dfs=.tres[2],conf.int1=.tres$conf.int[1],conf.int2=  .tres$conf.int[2],p.value=.tres[3])

      })

finalresults <- do.call(rbind, tresults)



(Thanks to Mark Leeds for the lapply approach)

>
> Hi Everyone,
>
> I need some simple help.
>
> Here are my codes
>
> ##########will give me 10000
> probesets####################
> data.sub =
>
data.matrix[order(variableprobe,decreasing=TRUE),][1:10000,]
> dim(data.sub)
> data_output<-write.table(data.sub, file =
> "c://data_output.csv", sep = ",",
> col.names = NA)
>
> When i export to excel, it shows me this. This is
> just a short version.
> There are 1000 rows and 140 columns
>
> Sample_1_D Sample_1_C Sample_2_D Sample_2_C
> 1 2.425509867 11.34031409 11.46868531 11.75741478
>
>
> Here is my question: How do create a new row and
> calculate the t-test so
> that it will give me the p-value
>
> Here is what i am looking for. The p-value is not
> correct but just an
> example. It needs to calculate the entire each row.
> There are 10000 rows and
> 140 columns.
>
> thanks
> Kei
>
> Sample_1_D Sample_1_C Sample_2_D Sample_2_C
> p-value
> 1 2.425509867 11.34031409 11.46868531 11.75741478
> .00341111
>
> I tried something like this.
>
> t.test(data.sub,mu=0)
>
> I am pretty new to R. I think it is showing me the
> entire p-value.
>
>
>
> --
> View this message in context:
>
http://www.nabble.com/Calculating-the-t-test-for-each-row-tp15808716p15808716.html
> Sent from the R help mailing list archive at
> Nabble.com.
>
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>



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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Mon 03 Mar 2008 - 18:27:36 GMT

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