[BioC] Simulation of the beta average
Shi, Tao
shidaxia at yahoo.com
Wed Sep 29 20:47:19 CEST 2010
Why can you generate simulation data by bootstrapping your existing data?
...Tao
----- Original Message ----
> From: Samor Gandhi <samorgandhi at yahoo.com>
> To: Sean Davis <sdavis2 at mail.nih.gov>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Sent: Tue, September 28, 2010 6:23:56 AM
> Subject: Re: [BioC] Simulation of the beta average
>
> Hi Sean,
>
> Thank you for your reply. What I posted would be for one sample, but I need to
>have let say 20 samples into two groups, that the first group would have
>different mean and standard deviation than the second group; and that was my
>problem how to generate these.
>
> I did something like
>
> S <- 10000
> n <- 10
> data1 <- c(runif(n*S*0.2,0,0.05),
>runif(n*S*0.6,0.06,0.95),runif(n*S*0.2,0.96,1))
> data2 <- c(runif(n*S*0.2,0.06,0.1),
>runif(n*S*0.6,0.11,0.8),runif(n*S*0.2,0.81,0.9))
>
> group1 <- matrix(data1, nrow = S,ncol = n)
> group2 <- matrix(data2, nrow = S,ncol = n)
>
> wt <- rep(NA, S)
> for (i in 1:S) {
> wt[i] <- wilcox.test(group1[i, ], group2[i, ], alternative =
>"two.sided")$p.value }
> Wsize <- sum(wt < 0.05)/S
> Wsize
>
> I very thankful for any help.
>
> Samor
>
> --- On Tue, 28/9/10, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
> From: Sean Davis <sdavis2 at mail.nih.gov>
> Subject: Re: [BioC] Simulation of the beta average
> To: "Samor Gandhi" <samorgandhi at yahoo.com>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Date: Tuesday, 28 September, 2010, 17:46
>
>
>
> On Tue, Sep 28, 2010 at 7:15 AM, Samor Gandhi <samorgandhi at yahoo.com> wrote:
>
> Hi Sean,
>
> I am trying to compute the power of the SAMr for t-test and Wilcoxon test!
>
>
>
> Hi, Samor.
> You might need to look into the data a bit more and perhaps review a bit about
>power calculation before proceeding further. There are a few steps missing, I
>think. What you posted doesn't constitute a simulation that could be used for
>power calculations unless I misunderstand what you are trying to do.
>
> Sean
>
> Regards,
> Samor
>
> --- On Tue, 28/9/10, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>
> From: Sean Davis <sdavis2 at mail.nih.gov>
> Subject: Re: [BioC] Simulation of the beta average
> To: "Samor Gandhi" <samorgandhi at yahoo.com>
>
> Cc: bioconductor at stat.math.ethz.ch
> Date: Tuesday, 28 September, 2010, 14:31
>
>
>
> On Tue, Sep 28, 2010 at 4:45 AM, Samor Gandhi <samorgandhi at yahoo.com> wrote:
>
>
> Hello,
>
>
>
> I would like to run a simulation study on the beta average of the Beta Studio
>illumin. I did something like x <- c(runif(200,0,0.1),
>runif(600,0.11,0.89),runif(200,0.9,1)); hist(x)! Would this be a reasonable
>simulation?
>
>
>
>
> Hi, Samor.
> I think the answer to your question is going to depend on what you mean by
>"reasonable" and that will depend on the question you are actually trying to
>answer. What is the question you are trying to answer? Are you trying to
>perform hypothesis testing or algorithm development, or something else?
>
>
> Sean
>
>
>
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