[R] How to calculate fold change and its confidence interval

[Steve Lianoglou]

Hi,

Firstly, you should bring your bioinformatics related questions over
to the bioconductor mailing list. Please sign up and post that portion
there, see:

http://www.bioconductor.org/docs/mailList.html

But, getting to your last question:

>> fc.perSample <- cbind(tb[,1]/tb[,3], tb[,2]/tb[,4])
>> fc.perSample
>        [,1]      [,2]
> [1,] 2.471264 1.1666667
> [2,] 2.475610 0.7045455
> [3,] 2.469565 1.6111111
> [4,] 2.421053 0.7529412
>
>> rowMeans(fc.perSample)
> [1] 1.818966 1.590078 2.040338 1.586997
>
> But if you manually check every gene one by one, totally different results
> were got. for example:
>> mean(2.471264, 1.1666667)
> [1] 2.471264

In short: you're doing it wrong.

You are passing 1.166 as the second parameter to the mean function.
See its help page to figure out what the params are: ?mean

You have to pass it in a *vector* of numbers to take the mean from:

R> mean(c(2.471264, 1.1666667))
[1] 1.818965

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact