[R] prcomp - arbitrary direction of the returned principal components

Ebert,Timothy Aaron tebert @end|ng |rom u||@edu
Thu Oct 13 14:03:17 CEST 2022

I still do not understand. However, the general approach would be to identify a specific value to test. If the test is TRUE then do "this" otherwise do nothing. Once the test condition is properly identified, the coding easily follows.

 abs() is the same as
if x<0 then x = -x   (non-R code, just idea)
The R code might look something more like
for (number in 1:ncol(x)){
   if (x[3,2] < 0) {
         x[number, number] = -x[number, number] #only change the diagonal

Depending on what values need to be changed you may need a nested for loop to go through all values of x[number1, number2]. 

Your words: " I can forcefully use a NEGATIVE sign to FLIP the index when it is LOW." Where it appeared that "low" was defined as values that are negative. You still will have low values (close to zero) and high values (far from zero). 

You could make the condition some other value:

if x< -4 then x = -x

If you just want to rotate about zero then 
x = -x
In this case the positive values will become negative and the negative values positive.
Add an if test to selectively rotate based on the value of a single test element in x (as in x[3,2]). 

In debugging or trouble shooting setting seed is useful. For actual data analysis you should not set seed, or possibly better yet use set.seed(NULL).


-----Original Message-----
From: Ashim Kapoor <ashimkapoor using gmail.com> 
Sent: Thursday, October 13, 2022 12:28 AM
To: Ebert,Timothy Aaron <tebert using ufl.edu>
Cc: R Help <r-help using r-project.org>
Subject: Re: [R] prcomp - arbitrary direction of the returned principal components

[External Email]

Dear Aaron,

Many thanks for your reply.

Please allow me to illustrate my query a bit.

I take some data, throw it to prcomp and extract the x data frame from prcomp.

>From ?prcomp:

       x: if 'retx' is true the value of the rotated data (the centred
          (and scaled if requested) data multiplied by the 'rotation'
          matrix) is returned.  Hence, 'cov(x)' is the diagonal matrix
          'diag(sdev^2)'.  For the formula method, 'napredict()' is
          applied to handle the treatment of values omitted by the

I consider x[,1] as my index. This makes sense as x[,1] is the projection of the data on the FIRST principal component.
Now this x[,1] can be a high +ve number or a low -ve number. I can't ignore the sign.

If I ignore the sign by taking the absolute value, the HIGH / LOW stress values will be indistinguishable.

Hence I do not think using absolute values of x[,1] is the solution.
Yes it will make the results REPRODUCIBLE but that will be at the cost of losing information.

Any other idea ?

Many thanks,

On Wed, Oct 12, 2022 at 5:23 PM Ebert,Timothy Aaron <tebert using ufl.edu> wrote:
> Use absolute value
> Tim
> -----Original Message-----
> From: R-help <r-help-bounces using r-project.org> On Behalf Of Ashim Kapoor
> Sent: Wednesday, October 12, 2022 7:48 AM
> To: R Help <r-help using r-project.org>
> Subject: [R] prcomp - arbitrary direction of the returned principal 
> components
> [External Email]
> Dear R experts,
> From ?prcomp,
> ---- snip -----
> Note:
>      The signs of the columns of the rotation matrix are arbitrary, and
>      so may differ between different programs for PCA, and even between
>      different builds of R.
> ---- snip ------
> My problem is that I am building an index based on Principal Components Analysis.
> When the index is high it should indicate stress in the market. Due to the arbitrary sign sometimes I get an index which is HIGH when there is stress and sometimes I get  the OPPOSITE - an index which is LOW when there is stress.
> This program is shared with other people who may have a different build of R.
> I can forcefully use a NEGATIVE sign to FLIP the index when it is LOW.
> That works.
> Now my query is : Just like we do set.seed(1234) and force the pattern of generation of random number and make it REPRODUCIBLE, can I do something like :
> set.direction.for.vector.in.pca(1234)
> Now each time I do prcomp it should choose the SAME ( high or low ) direction of the principle component on ANY computer having ANY version of R installed.
> That's what I want. I don't want the the returned principal component to be HIGH(LOW) on my computer and LOW(HIGH) on someone else's computer.
> That would confuse the people the code is shared with.
> Is this possible ? How do people deal with this ?
> Many thanks,
> Ashim
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