Yes, Bert, you are right and I do know I might run into a non-positive
definite intercorrelation matrix.
But if I do, then I can go back to those for whom I am doing the analysis
and tell them that. Not before.
This sad truth being said - can I do it directly in the function, without
building a intercorrelation matrix manually?
Thank you!
Dimitri

On Wed, Mar 20, 2013 at 7:04 PM, Bert Gunter <gunter.berton@gene.com> wrote:

> Well, you can do this, but there's no guarantee that the resulting
> correlation matrix will be positive definite. And what would principle
> components based on this mean even if it is positive definite?
>
> -- Bert
>
>  On Wed, Mar 20, 2013 at 3:14 PM, Dimitri Liakhovitski <
> dimitri.liakhovitski@gmail.com> wrote:
>
>>  Hello!
>> I am running principle components analysis using princomp function in
>> pacakge psych.
>>
>> mypc <- princomp(mydataforpc, cor=TRUE)
>>
>> Question: I'd like to use pairwise deletion of missing cases when
>> correlations are calculated. I.e., I'd like to have a correlation between
>> any 2 variables to be based on all cases that have valid values on both
>> variables.
>>
>> What should my na.action be in this case?
>>
>> Thank you very much!
>> --
>> Dimitri Liakhovitski
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@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<http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
>
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
>



-- 
Dimitri Liakhovitski

	[[alternative HTML version deleted]]

