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.
You can try this: cbind(data.sub, p.value=apply(data.sub, 1, function(x)t.test(x)$p.value)) On 03/03/2008, Keizer_71 <christophe.lo at gmail.com> wrote:> > 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. > > ______________________________________________ > R-help at r-project.org mailing list > 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. >-- Henrique Dallazuanna Curitiba-Paran?-Brasil 25? 25' 40" S 49? 16' 22" O
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)
--- Keizer_71 <christophe.lo at gmail.com> wrote:
>
> 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.
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>
Using t.test() in this case will likely be very slow. A faster alternative would be to use rowttests() from the genefilter package of Bioconductor. Best, Jim Henrique Dallazuanna wrote:> You can try this: > > cbind(data.sub, p.value=apply(data.sub, 1, function(x)t.test(x)$p.value)) > > On 03/03/2008, Keizer_71 <christophe.lo at gmail.com> wrote: >> 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. >> >> ______________________________________________ >> R-help at r-project.org mailing list >> 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. >> > >-- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623