Jim,
Thank you for your reply. I guess I am just not understanding what the
difference is. If I run your example using the
pcmatrix<-data.frame(Q1=sample(1:5,10,TRUE),Q2=sample(1:5,10,TRUE)) and print
out pcmatrix I get:
Q1 Q2
1 98 99
Then if I mirror my input file to be, would would be what the samples from
above would have created, it would look like this:
ID,Q1,Q2
1,2,3
And I run the script printing out pcmatrix I get the exact same thing.
Q1 Q2
1 98 99
So I would think they are basically the same representations, however one works
when passed into the prcomp function and the other does not. I am just trying
to tweak a script that we had created for us (cannot find the guy now) so I can
pass more columns of data. I clearly really do not know what I am doing, but
again thanks for you time and any direction you can point me in would be
awesome.
Thanks
Jason
On Nov 1, 2012, at 3:57 AM, Jim Lemon wrote:
> On 10/31/2012 11:47 PM, fillay89 wrote:
>> I am trying to run the R Script below, I have actually simplified it to just
>> this part that is causing issues. When I run this script I continue to get
>> an error that says "cannot rescale a constant/zero column to a unit
>> variance". I cannot figure out what is going on here. I have stripped down
>> my data file so it is more manageable so I can try to figure this out.
>>
>> The data.txt file that is being read looks like this:
>>
>>
>> I have made this file very basic on purpose to see if I could get this to
>> work, but it is not working. Of course once I get this to actually work I
>> will expand the data file to match the data I am actually using.
>>
>>
>>
>> If I change the attribute in the prcomp function to scale=FALSE of course I
>> can run my script. But if it is scaling...which is causing the issues, it
>> errors.
>>
>> Any help would be GREATLY appreciated.
>>
> Hi fillay89,
> You seem to be trying to run a principal component analysis on two numbers,
> which won't produce anything useful. If I make up some data that is more
> realistic:
>
> pcmatrix<-data.frame(Q1=sample(1:5,10,TRUE),Q2=sample(1:5,10,TRUE))
> pcmatrix[,1] <- pcmatrix[,1] + 96
> pcmatrix[,2] <- pcmatrix[,2] + 96
> x.pca <- prcomp(pcmatrix,retx=TRUE,center=TRUE,scale=TRUE,cor=TRUE)
> x.pca
> Standard deviations:
> [1] 1.263267 0.635733
>
> Rotation:
> PC1 PC2
> Q1 0.7071068 -0.7071068
> Q2 0.7071068 0.7071068
>
> it runs and I get a slightly more useful result. Running your code does bomb
> in exactly the way you describe, as does:
>
> x.pca <- prcomp(data.frame(Q1=99,Q2=98), retx=TRUE, center=TRUE, scale=TRUE,
> cor=TRUE)
> Error in prcomp.default(data.frame(Q1 = 99, Q2 = 98), retx = TRUE, center =
> TRUE, :
> cannot rescale a constant/zero column to unit variance
>
> Your problem is that you have a data frame with only one value (i.e. a
> constant) in each column.
>
> Jim
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