Hello,
I'd like to think all respondents for your advises and suggestions. I am sorry
for not including the ordered gene expression data frame (largedf) since it is
large.
The problem is solved now by Greg Down by including the command:
rm(.Random.seed) in the code, perhaps I used some R packges to process that
expression data which set the seed on the Random Number Generator to a fixed
value.
Thanks again,
Joshua
----- Original Message -----
From: "Charles C. Berry" <[EMAIL PROTECTED]>
To: "Shuhua Zhan" <[EMAIL PROTECTED]>
Cc: r-help@r-project.org
Sent: Thursday, October 30, 2008 9:07:09 PM GMT -05:00 US/Canada Eastern
Subject: Re: [R] why does sample(x, n) give the same n items in every separate
runs?
Run help.request().
In particular you need to attend to this part:
Have you written example code that is
- minimal
- reproducible
- self-contained
- commented
using data that is either
- constructed by the code
- loaded by data()
- reproduced using dump("mydata", file = "")
have you checked this code in a fresh R session (invoking R with the
--vanilla option if possible) and is this code copied to the clipboard? (y/n)
----
Once you get this far and can honestly type 'y', if you have not found
your error, you are ready to post a query.
HTH,
Chuck
On Thu, 30 Oct 2008, Shuhua Zhan wrote:
> Hello R users,
> I have gene expression data of two groups of genes (large and small). Gene
> expression intensities of those genes are classified into 1 to 10 levels.
> What I want is to make a random set of genes that have the same levels as the
> small group from large group using sample().
>
> I used smallvec to hold the number of genes in each levels (1 to 10) for
> small group, largevec for large group. I ordered the gene expression data
> frame of large group (largedf) by the levels and randomly chose the genes
> with same level as small group. Using the code below I can get the random set
> of genes from lagre group with same levels for small group. But I got the
> same set of genes when I run the code in every other runs in Linux. This
> gives me a doubt in my result.
>
> smallvec<-c(8,12,9,6,13,20,16,11,8,5) ## the No. of genes in levels 1 to 10
> largevec<-c(400,300,550,600,210,420,380,600,450,500)
> generdm<-c() ## a random set of genes
> for( i in 1:length(smallvec)){
>
> generdm<-c(generdm,sample(rownames(largedf)[sum(largevec[0:(i-1)],1):sum(largevec[0:i])],smallvec[i]))
> ## rownames(largedf) gives gene names ordered by levels in large group
> }
>
> Could you please help me out?
> Thanks a lot!!
> Josh
>
> ______________________________________________
> R-help@r-project.org mailing list
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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.
>
Charles C. Berry (858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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