Help on Principal Component Analysis in R

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Help on Principal Component Analysis in R

R Help!
Hello!

I am a beginner to R. I have read several guides, but still am stuck on
this:

I have data in an excel csv file, on which I want to run PCA.
I'm not sure how the prcomp formula works. The help page states:
prcomp(x, retx = TRUE, center = TRUE, scale. = FALSE,
tol = NULL, ...)

what is x referring to? I tried putting the file name for x, but i get the
following error:
Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric

what kind of numeric value do I need to put in for x?

Potentially helpful information: my data sheet has around 48 columns and
over 7000 rows. I have converted the csv file into a matrix in R.

Thanks in advance for all your help.

I'd appreciate step by step instructions on how to go from my csv file to a
PCA biplot in R.

        [[alternative HTML version deleted]]

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Re: Help on Principal Component Analysis in R

Jeff Newmiller
I'd you keep reading the help file, the answer to your question is right there.

As for step by step... only you know what your data looks like. There are various pitfalls one can encounter in getting data from a file into an object in memory, but the basic idea is to use the read.csv function, and then optionally the str function to verify that it has been read in properly. There is a whole document that comes with R to show you how to get data into and out of R, and a reproducible example is needed if we are to be able to give specific guidance. [1]

Oh and there is a Posting Guide that you should read mentioned at the bottom if this and every message on the list. Among the valuable nuggets in there is a statement that this is a plain text mailing list (HTML email gets stripped to text do we don't necessarily see what you see), so please send plain text only so you know what we will see.

[1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
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On January 13, 2015 3:17:11 PM PST, R Help! <[hidden email]> wrote:

>Hello!
>
>I am a beginner to R. I have read several guides, but still am stuck on
>this:
>
>I have data in an excel csv file, on which I want to run PCA.
>I'm not sure how the prcomp formula works. The help page states:
>prcomp(x, retx = TRUE, center = TRUE, scale. = FALSE,
>tol = NULL, ...)
>
>what is x referring to? I tried putting the file name for x, but i get
>the
>following error:
>Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric
>
>what kind of numeric value do I need to put in for x?
>
>Potentially helpful information: my data sheet has around 48 columns
>and
>over 7000 rows. I have converted the csv file into a matrix in R.
>
>Thanks in advance for all your help.
>
>I'd appreciate step by step instructions on how to go from my csv file
>to a
>PCA biplot in R.
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Help on Principal Component Analysis in R

Karim Mezhoud
In reply to this post by R Help!
Hi error message indicates that you have non numeric value in your table/
matrix. Replace missing value by NA and add na.rm= true in your command
prcomp.
Karim
Le 14 janv. 2015 00:27, "R Help!" <[hidden email]> a écrit :

> Hello!
>
> I am a beginner to R. I have read several guides, but still am stuck on
> this:
>
> I have data in an excel csv file, on which I want to run PCA.
> I'm not sure how the prcomp formula works. The help page states:
> prcomp(x, retx = TRUE, center = TRUE, scale. = FALSE,
> tol = NULL, ...)
>
> what is x referring to? I tried putting the file name for x, but i get the
> following error:
> Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric
>
> what kind of numeric value do I need to put in for x?
>
> Potentially helpful information: my data sheet has around 48 columns and
> over 7000 rows. I have converted the csv file into a matrix in R.
>
> Thanks in advance for all your help.
>
> I'd appreciate step by step instructions on how to go from my csv file to a
> PCA biplot in R.
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Help on Principal Component Analysis in R

Christian Brandstätter
In reply to this post by R Help!
Hi,

it could also be that during reading your csv the matrix became a character
matrix.
Try str(x); this should show you if your values are seen as numeric.
Also, if you have descriptive columns (e.g. date, labels, etc.) they must
be removed before calculating PCR.

With best regards
Brandstätter Christian

2015-01-14 0:17 GMT+01:00 R Help! <[hidden email]>:

> Hello!
>
> I am a beginner to R. I have read several guides, but still am stuck on
> this:
>
> I have data in an excel csv file, on which I want to run PCA.
> I'm not sure how the prcomp formula works. The help page states:
> prcomp(x, retx = TRUE, center = TRUE, scale. = FALSE,
> tol = NULL, ...)
>
> what is x referring to? I tried putting the file name for x, but i get the
> following error:
> Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric
>
> what kind of numeric value do I need to put in for x?
>
> Potentially helpful information: my data sheet has around 48 columns and
> over 7000 rows. I have converted the csv file into a matrix in R.
>
> Thanks in advance for all your help.
>
> I'd appreciate step by step instructions on how to go from my csv file to a
> PCA biplot in R.
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.