R help - May 2009 - Using apply() and scale() in combination

Hello

I am an R newbie, and am coming against a couple of problems when I try and
apply the scale function across all the rows of a  matrix.

-------------------------
#I have a matrix "dt_l".
> str(dt_l)
 num [1:40962, 1:885] 3.04 4.1 3.4 3.58 3.77 ...

#I want to convert the values in each row of this matrix into standardised
values (mean 0, sd 1). I believe the command for doing this is
"scale()",
with the defaults for this function being to set mean at 0 and sd at 1.
Therefore, my desired end-point is an object with the same dimensions as
dt_l.

So, I use this command..which I think should applying scale to every row of
matrix dt_l:
> dt.stand<-apply(dt_l, 1, scale)
#This has led to two different sorts of problem:

(1) On some occasions when I have run the command I get an error warning
which includes the phrase

"error: can't allocate region..."

(2) On other occasions (when as far as I know I have entered the same
command), it runs. BUT, when I look at the object produced the dimensions
are different from dt_l ....
> str(dt.stand_l)
 num [1:885, 1:40962] -0.679 -0.0882 0.1204 1.8571 0.8854 ...

----------------------------

I would be very grateful for any explanations/fixes that can be offered for
the above, or any suggestions of alternative ways of reaching my desired
end-point.

Yours hopefully

Armin

Tena koe Armin

From the help file of apply():

     If each call to 'FUN' returns a vector of length 'n', then
'apply'
     returns an array of dimension 'c(n, dim(X)[MARGIN])' if 'n >
1'.
  
So, one should expect what you got in the second case.  You can, of
course, transpose the result using t().

HTH .....

Peter Alspach
> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Armin Raznahan
> Sent: Tuesday, 19 May 2009 9:44 a.m.
> To: r-help at r-project.org
> Subject: [R] Using apply() and scale() in combination
> 
> Hello
> 
> I am an R newbie, and am coming against a couple of problems 
> when I try and apply the scale function across all the rows 
> of a  matrix.
> 
> -------------------------
> #I have a matrix "dt_l".
> 
> > str(dt_l)
>  num [1:40962, 1:885] 3.04 4.1 3.4 3.58 3.77 ...
> 
> #I want to convert the values in each row of this matrix into 
> standardised values (mean 0, sd 1). I believe the command for 
> doing this is "scale()", with the defaults for this function 
> being to set mean at 0 and sd at 1.
> Therefore, my desired end-point is an object with the same 
> dimensions as dt_l.
> 
> So, I use this command..which I think should applying scale 
> to every row of matrix dt_l:
> 
> > dt.stand<-apply(dt_l, 1, scale)
> 
> #This has led to two different sorts of problem:
> 
> (1) On some occasions when I have run the command I get an 
> error warning which includes the phrase
> 
> "error: can't allocate region..."
> 
> (2) On other occasions (when as far as I know I have entered 
> the same command), it runs. BUT, when I look at the object 
> produced the dimensions are different from dt_l ....
> 
> > str(dt.stand_l)
>  num [1:885, 1:40962] -0.679 -0.0882 0.1204 1.8571 0.8854 ...
> 
> ----------------------------
> 
> I would be very grateful for any explanations/fixes that can 
> be offered for the above, or any suggestions of alternative 
> ways of reaching my desired end-point.
> 
> Yours hopefully
> 
> Armin
> 
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> PLEASE do read the posting guide 
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