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Newbie: Incorrect number of dimensions

5 messages · Keizer_71, jim holtman, Henrique Dallazuanna +1 more

Keizer_71
# 
[1] 10000   140

#####extracting all differentially express genes##########
library(multtest)
two_side<- (1-pt(abs(data.sub),50))*2
diff<- mt.rawp2adjp(two_side)
all_differ<-diff[[1]][37211:10000,]
all_differ

#####list of differentially expressed genes##########
+ all_differ[[2]][all_differ[[1]][,"BY"]<=0.01]

Error in all_differ[[1]][, "BY"] : incorrect number of dimensions

Hi,

I am pretty new with R. What i am trying to do is to find all differentially
express genes and list of differentially expressed genes. Am i doing
something wrong?

I keep getting incorrect number of dimensions. How do i find out the correct
dimensions? 

thanks,
Keizer
jim holtman
# 
It would be helpful if you provided commented, minimal,
self-contained, reproducible code.

What does str(all_differ) say?  That will tell you the structure of
the object that you are trying to work with.
On Sat, Mar 1, 2008 at 3:35 AM, Keizer_71 <christophe.lo at gmail.com> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Keizer_71
    

    

      
      #
    

  


  

      
Here is the structure

            

      
      
      
    

        
num [1:6280, 1:8] 2.22e-16 2.22e-16 2.22e-16 2.22e-16 2.22e-16 ...
 - attr(*, "dimnames")=List of 2
  ..$ : NULL
  ..$ : chr [1:8] "rawp" "Bonferroni" "Holm" "Hochberg" ...

I tried, but it still giving me the same error message "Incorrect Dimension"

probe.names<-all_differ[[1]][all_differ[[6280]][,"BY"]<=0.01]

Am i using the wrong dimension?

thanks,
Keizer

        
jholtman wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Henrique Dallazuanna
    

    

      
      #
    

  


  

      
You have a 'matrix' not a 'list', so
I think you want something like this:

all_differ[all_differ[, 'BY'] <= 0.01, 'BY'], this will return the
values where column is 'BY' in all rows which is less or equal to
0.01.

        
On 02/03/2008, Keizer_71 <christophe.lo at gmail.com> wrote: