[R] t.test p-Value

2008-03-05 Thread Eleni Christodoulou 
Hello list,

I am trying to apply the paired t.test between diseased and not diseased
patients to identify genes that are more expressed in the one situation
under the other. In order to retrieve the genes that are more expressed in
the positive disease state I do:
p.values-c()
for(i in 1:length(Significant[,1])){
p.values[i]-try(t.test(positive[i,],negative[i,],alternative
=greater)$p.value)
}

which(p.values0.01)


where Significant is my matrix of  genes  and their expression in tumors and
positive, negative are subsets of thes matrix.
Whn p0.01, I reject the null hypothesis and I accept the alternative one,
that I have greater gene expression in positive than in negative.
I assume I must be doing sth wrong because the heatmap that I get with the
genes that pass the filter of p-value is wrong.

Could anyone help me with this?

thanks a lot,
Eleni

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Re: [R] t.test p-Value

2008-03-05 Thread Eleni Christodoulou 
I am sorry, the test is unpaired...But my question remains

Thanks,
Eleni

On Wed, Mar 5, 2008 at 2:33 PM, Eleni Christodoulou [EMAIL PROTECTED]
wrote:

 Hello list,

 I am trying to apply the paired t.test between diseased and not diseased
 patients to identify genes that are more expressed in the one situation
 under the other. In order to retrieve the genes that are more expressed in
 the positive disease state I do:
 p.values-c()
 for(i in 1:length(Significant[,1])){
 p.values[i]-try(t.test(positive[i,],negative[i,],alternative
 =greater)$p.value)
 }

 which(p.values0.01)


 where Significant is my matrix of  genes  and their expression in tumors
 and positive, negative are subsets of thes matrix.
 Whn p0.01, I reject the null hypothesis and I accept the alternative one,
 that I have greater gene expression in positive than in negative.
 I assume I must be doing sth wrong because the heatmap that I get with the
 genes that pass the filter of p-value is wrong.

 Could anyone help me with this?

 thanks a lot,
 Eleni



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R-help@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] t.test p-Value

2008-03-05 Thread Eleni Christodoulou 
On Wed, Mar 5, 2008 at 2:05 PM, ian white [EMAIL PROTECTED] wrote:

 Don't you need to make some allowance for multiple testing? E.g. to get
 a experiment-wise significance level of 0.01 you need

 which(p.values  very small number)

 where the very small number is approximately 0.01/(total number of
 genes).

 On Wed, 2008-03-05 at 14:38 +0200, Eleni Christodoulou wrote:
  I am sorry, the test is unpaired...But my question remains
 
  Thanks,
  Eleni
 
  On Wed, Mar 5, 2008 at 2:33 PM, Eleni Christodoulou [EMAIL PROTECTED]
 
  wrote:
 
   Hello list,
  
   I am trying to apply the paired t.test between diseased and not
 diseased
   patients to identify genes that are more expressed in the one
 situation
   under the other. In order to retrieve the genes that are more
 expressed in
   the positive disease state I do:
   p.values-c()
   for(i in 1:length(Significant[,1])){
   p.values[i]-try(t.test(positive[i,],negative[i,],alternative
   =greater)$p.value)
   }
  
   which(p.values0.01)
  
  
   where Significant is my matrix of  genes  and their expression in
 tumors
   and positive, negative are subsets of thes matrix.
   Whn p0.01, I reject the null hypothesis and I accept the alternative
 one,
   that I have greater gene expression in positive than in negative.
   I assume I must be doing sth wrong because the heatmap that I get with
 the
   genes that pass the filter of p-value is wrong.
  
   Could anyone help me with this?
  
   thanks a lot,
   Eleni
  
  
 
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  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.
 



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and provide commented, minimal, self-contained, reproducible code.