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

From: James W. MacDonald <jmacdon_at_med.umich.edu>
Date: Mon, 03 Mar 2008 15:01:52 -0500

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.
>>
>> ______________________________________________
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>>
>
>
-- 
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

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Received on Mon 03 Mar 2008 - 20:03:12 GMT

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