R help - Nov 2007 - Reg : using two different matrix : how to do t.test

I have two matrix with same dimensions. I want to do t.test using each column
from 2 different matrix.
Row n Column names in both matrix are same. 
 
e.g.  
Matrix1       
id VC1 VC2 VC3       
R 1 2 3    
R1 4 5 6    
R3 7 8 9   
 
 
Matrix2    
id VC1 VC2 VC3 
R 10 11 12 
R1 13 14 15 
R3 16 17 18 
 
want to do t.test using each column (with same name ) using Matrix1 and Matrix2
 
for eg t.test(Matrix1$VC1, Matrix2$VC1)$p.value 
 
What is the best way to do it. I have dataset with 4000 columns for each matrix
with same row and column names.
 
Thanks a lot.
       
---------------------------------
Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now.
	[[alternative HTML version deleted]]

Hi

r-help-bounces at r-project.org napsal dne 19.11.2007 09:32:25:
> I have two matrix with same dimensions. I want to do t.test using each 
column 
> from 2 different matrix. 
> Row n Column names in both matrix are same. 
> 
> e.g. 
> Matrix1 
> id VC1 VC2 VC3 
> R 1 2 3 
> R1 4 5 6 
> R3 7 8 9 
> 
> 
> Matrix2 
> id VC1 VC2 VC3 
> R 10 11 12 
> R1 13 14 15 
> R3 16 17 18 
> 
> want to do t.test using each column (with same name ) using Matrix1 and 
Matrix2
> 
> for eg t.test(Matrix1$VC1, Matrix2$VC1)$p.value 
I am not sure if it is a best way but here seems to me that for cycle 
could be considered

result<-rep(NA, 3999)
for (i in 2:4000) {
result [i-1] <- t.test(mat1[,i], mat2[,i])$p.value
}

Regards
Petr
> 
> What is the best way to do it. I have dataset with 4000 columns for each 
> matrix with same row and column names. 
> 
> Thanks a lot.
> 
> ---------------------------------
> Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try 
it now.
>    [[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Hi Thanks for the reply.

I implemented your solution to my problem but ...

For some of my column there is not enough data to do t-test so it gives me
error and stops the for loop, is any graceful way to check for error msg and
say ok if there is no $p.value continue to the next column

Once again thx for help.



sata pinal wrote:
> 
> I have two matrix with same dimensions. I want to do t.test using each
> column from 2 different matrix.  
> Row n Column names in both matrix are same. 
>  
> e.g.  
> Matrix1       
> id VC1 VC2 VC3       
> R 1 2 3    
> R1 4 5 6    
> R3 7 8 9   
>  
>  
> Matrix2    
> id VC1 VC2 VC3 
> R 10 11 12 
> R1 13 14 15 
> R3 16 17 18 
>  
> want to do t.test using each column (with same name ) using Matrix1 and
> Matrix2
>  
> for eg t.test(Matrix1$VC1, Matrix2$VC1)$p.value 
>  
> What is the best way to do it. I have dataset with 4000 columns for each
> matrix with same row and column names. 
>  
> Thanks a lot.
>        
> ---------------------------------
> Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try
> it now.
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 
-- 
View this message in context:
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Sent from the R help mailing list archive at Nabble.com.

mogra wrote:
> Hi Thanks for the reply.
> 
> I implemented your solution to my problem but ...
> 
> For some of my column there is not enough data to do t-test so it gives me
> error and stops the for loop, is any graceful way to check for error msg
and
> say ok if there is no $p.value continue to the next column

See ?try

Uwe Ligges
> Once again thx for help.
> 
> 
> 
> sata pinal wrote:
>> I have two matrix with same dimensions. I want to do t.test using each
>> column from 2 different matrix.  
>> Row n Column names in both matrix are same. 
>>  
>> e.g.  
>> Matrix1       
>> id VC1 VC2 VC3       
>> R 1 2 3    
>> R1 4 5 6    
>> R3 7 8 9   
>>  
>>  
>> Matrix2    
>> id VC1 VC2 VC3 
>> R 10 11 12 
>> R1 13 14 15 
>> R3 16 17 18 
>>  
>> want to do t.test using each column (with same name ) using Matrix1 and
>> Matrix2
>>  
>> for eg t.test(Matrix1$VC1, Matrix2$VC1)$p.value 
>>  
>> What is the best way to do it. I have dataset with 4000 columns for
each
>> matrix with same row and column names. 
>>  
>> Thanks a lot.
>>        
>> ---------------------------------
>> Be a better sports nut! Let your teams follow you with Yahoo Mobile.
Try
>> it now.
>> 	[[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>

Since t.test takes much more time than parsing loop, I
won't hesitate to do a loop on the columns.

--- sata pinal <satapinal at yahoo.com> wrote:
> I have two matrix with same dimensions. I want to do
> t.test using each column from 2 different matrix.  
> Row n Column names in both matrix are same. 
>  
> e.g.  
> Matrix1       
> id VC1 VC2 VC3       
> R 1 2 3    
> R1 4 5 6    
> R3 7 8 9   
>  
>  
> Matrix2    
> id VC1 VC2 VC3 
> R 10 11 12 
> R1 13 14 15 
> R3 16 17 18 
>  
> want to do t.test using each column (with same name
> ) using Matrix1 and Matrix2
>  
> for eg t.test(Matrix1$VC1, Matrix2$VC1)$p.value 
>  
> What is the best way to do it. I have dataset with
> 4000 columns for each matrix with same row and
> column names. 
>  
> Thanks a lot.
>        
> ---------------------------------
> Be a better sports nut! Let your teams follow you
> with Yahoo Mobile. Try it now.
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained,
> reproducible code.
>

sapply(1:4000, function(k){
   t.test(Matrix1[,k], Matrix2[,k])$p.value
})


I did not test, though.

HTH,

Weiwei

On 11/19/07, sata pinal <satapinal at yahoo.com>
wrote:
> I have two matrix with same dimensions. I want to do t.test using each
column from 2 different matrix.
> Row n Column names in both matrix are same.
>
> e.g.
> Matrix1
> id VC1 VC2 VC3
> R 1 2 3
> R1 4 5 6
> R3 7 8 9
>
>
> Matrix2
> id VC1 VC2 VC3
> R 10 11 12
> R1 13 14 15
> R3 16 17 18
>
> want to do t.test using each column (with same name ) using Matrix1 and
Matrix2
>
> for eg t.test(Matrix1$VC1, Matrix2$VC1)$p.value
>
> What is the best way to do it. I have dataset with 4000 columns for each
matrix with same row and column names.
>
> Thanks a lot.
>
> ---------------------------------
> Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it
now.
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

Hi

r-help-bounces at r-project.org napsal dne 20.11.2007 09:36:32:
> 
> Hi Thanks for the reply.
> 
> I implemented your solution to my problem but ...
> 
> For some of my column there is not enough data to do t-test so it gives 
me
> error and stops the for loop, is any graceful way to check for error msg 
and
> say ok if there is no $p.value continue to the next column
You need at least 2 values for x and 2 values for y so you can just put an 
if clause in your for loop. Something like:

for (whatever) {
if(sum(!is.na(x)>1 & sum(!is.na(y)>1) do your t.test
}

Regards
Petr

> 
> Once again thx for help.
> 
> 
> 
> sata pinal wrote:
> > 
> > I have two matrix with same dimensions. I want to do t.test using each
> > column from 2 different matrix. 
> > Row n Column names in both matrix are same. 
> > 
> > e.g. 
> > Matrix1 
> > id VC1 VC2 VC3 
> > R 1 2 3 
> > R1 4 5 6 
> > R3 7 8 9 
> > 
> > 
> > Matrix2 
> > id VC1 VC2 VC3 
> > R 10 11 12 
> > R1 13 14 15 
> > R3 16 17 18 
> > 
> > want to do t.test using each column (with same name ) using Matrix1 
and
> > Matrix2
> > 
> > for eg t.test(Matrix1$VC1, Matrix2$VC1)$p.value 
> > 
> > What is the best way to do it. I have dataset with 4000 columns for 
each
> > matrix with same row and column names. 
> > 
> > Thanks a lot.
> > 
> > ---------------------------------
> > Be a better sports nut! Let your teams follow you with Yahoo Mobile. 
Try
> > it now.
> >    [[alternative HTML version deleted]]
> > 
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> > 
> > 
> 
> -- 
> View this message in context: 
http://www.nabble.com/Reg-%3A-%09using-two-
> different-matrix-%3A-how-to-do-t.test-tf4834072.html#a13845405
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.