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

From: Benilton Carvalho <bcarvalh_at_jhsph.edu>
Date: Mon, 03 Mar 2008 13:26:10 -0500

apparently you want to check the genefilter package...

it defines functions like:

rowttests
colttests
rowFtests
colFtests
rowVars
rowSds

moreover, a quick look at Biobase is recommended...

that would save you lots of time as you wouldn't have to reinvent the wheel.

b

On Mar 3, 2008, at 12:42 PM, 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.
>>
>
>
> --
> Henrique Dallazuanna
> Curitiba-Paraná-Brasil
> 25° 25' 40" S 49° 16' 22" O
>
> ______________________________________________
> 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.



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