[R] Calculating the t-test for each row

[James W. MacDonald]

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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>>  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