Hi Adai,

It works!! Thanks a lot!!

Hui-Yi


On Fri, Sep 12, 2008 at 11:26 AM, Adaikalavan Ramasamy <
a.ramasamy@imperial.ac.uk> wrote:

> help(rowttests) says that fac needs to be a factor. So how about ?
>
>  m <- matrix( rnorm(30), nc=6 )
>  genotype <- c("a", "a", "b", "b", "c", "c")
>
>  w1 <- which( genotype %in% c("a", "b") )
>  w2 <- which( genotype %in% c("a", "c") )
>  w3 <- which( genotype %in% c("b", "c") )
>
>  list( ab = rowttests( m[ , w1], factor( genotype[w1] ) ),
>        ac = rowttests( m[ , w2], factor( genotype[w2] ) ),
>        bc = rowttests( m[ , w3], factor( genotype[w3] ) ) )
>
> Regards, Adai
>
>
>
> Hui-Yi Chu wrote:
>
>> Dear R list,
>>
>> I think my question maybe easy for you but I really spent entire day to
>> resolve it.
>> Say I have a matrix, rows are 6000 genes, columns(1-6) are 3 genotypes
>> (a,b,c) with 2 repeat.
>> I have to use two groups each time for t-test, a vs. c or b vs. c, but I
>> dont know how to write correct codes.
>> Below is my codes, the last two lines are needed to be corrected....
>>
>> library("genefilter")
>> ef <- exprs(esetsub)
>> kk <- factor(esetsub$genotype == c("a", "c"))
>> tt <- rowttests(ef[,c(1,2,5,6)], kk)
>>
>> ps.  column 1-6 is a,a,b,b,c,c
>>      depending on the document, the kk should be a factor..
>>
>> Any suggestions are really appreciated!!
>>
>> Best regards,
>> Hui-Yi
>>
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>>
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>>
>
>

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