[R] Different PCA results under Windows and Linux
jathine
jathine.wong at utah.edu
Wed Sep 17 19:12:51 CEST 2008
Thank you for your reply.
Here are some more info, I hope this can explain the problem a bit more
clearly.
Why PCA gives different results on the two different platforms?
freqtest.txt file line text :
M1 M2 M3 M4 M5 M6 M7 M8
-1 -1 -1 -1 -1 -1 -1 -1
0 0 0 0 -1 -1 1 1
-1 -1 -1 -1 -1 -1 -1 -1
0 0 0 0 -1 -1 1 1
******Linux R script result and sessionInfo()
> library(FactoMineR)
> x1=read.table("freqtest.txt", header=TRUE)
> xrcc2=x1[,1:8]
> p1=PCA(xrcc2, graph=FALSE)
> p1$var
$coord
Dim.1 Dim.2 Dim.3
M1 1 -3.925231e-16 -2.287663e-48
M2 1 7.850462e-17 -3.600641e-32
M3 1 7.850462e-17 9.001602e-33
M4 1 7.850462e-17 9.001602e-33
M5 0 0.000000e+00 0.000000e+00
M6 0 0.000000e+00 0.000000e+00
M7 1 7.850462e-17 9.001602e-33
M8 1 7.850462e-17 9.001602e-33
$cor
Dim.1 Dim.2 Dim.3
M1 1 -3.925231e-16 -2.287663e-48
M2 1 7.850462e-17 -3.600641e-32
M3 1 7.850462e-17 9.001602e-33
M4 1 7.850462e-17 9.001602e-33
M5 NaN NaN NaN
M6 NaN NaN NaN
M7 1 7.850462e-17 9.001602e-33
M8 1 7.850462e-17 9.001602e-33
$cos2
Dim.1 Dim.2 Dim.3
M1 1 1.540744e-31 5.233404e-96
M2 1 6.162976e-33 1.296462e-63
M3 1 6.162976e-33 8.102884e-65
M4 1 6.162976e-33 8.102884e-65
M5 NaN NaN NaN
M6 NaN NaN NaN
M7 1 6.162976e-33 8.102884e-65
M8 1 6.162976e-33 8.102884e-65
$contrib
Dim.1 Dim.2 Dim.3
M1 16.66667 83.333333 3.229346e-31
M2 16.66667 3.333333 8.000000e+01
M3 16.66667 3.333333 5.000000e+00
M4 16.66667 3.333333 5.000000e+00
M5 0.00000 0.000000 0.000000e+00
M6 0.00000 0.000000 0.000000e+00
M7 16.66667 3.333333 5.000000e+00
M8 16.66667 3.333333 5.000000e+00
> sessionInfo()
R version 2.7.1 (2008-06-23)
x86_64-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] FactoMineR_1.09
>
******Windows R script result and sessionInfo()
> library(FactoMineR)
> x1=read.table("freqtest.txt", header=TRUE)
> xrcc2=x1[,1:8]
> p1=PCA(xrcc2, graph=FALSE)
> p1$var
$coord
Dim.1 Dim.2 Dim.3
M1 1 2.458061e-16 -4.590163e-49
M2 1 -4.916122e-17 -4.750455e-32
M3 1 -4.916122e-17 1.187614e-32
M4 1 -4.916122e-17 1.187614e-32
M5 0 0.000000e+00 0.000000e+00
M6 0 0.000000e+00 0.000000e+00
M7 1 -4.916122e-17 1.187614e-32
M8 1 -4.916122e-17 1.187614e-32
$cor
Dim.1 Dim.2 Dim.3
M1 1 2.458061e-16 -4.590163e-49
M2 1 -4.916122e-17 -4.750455e-32
M3 1 -4.916122e-17 1.187614e-32
M4 1 -4.916122e-17 1.187614e-32
M5 NaN NaN NaN
M6 NaN NaN NaN
M7 1 -4.916122e-17 1.187614e-32
M8 1 -4.916122e-17 1.187614e-32
$cos2
Dim.1 Dim.2 Dim.3
M1 1 6.042064e-32 2.106959e-97
M2 1 2.416826e-33 2.256682e-63
M3 1 2.416826e-33 1.410426e-64
M4 1 2.416826e-33 1.410426e-64
M5 NaN NaN NaN
M6 NaN NaN NaN
M7 1 2.416826e-33 1.410426e-64
M8 1 2.416826e-33 1.410426e-64
$contrib
Dim.1 Dim.2 Dim.3
M1 16.66667 83.333333 7.469228e-33
M2 16.66667 3.333333 8.000000e+01
M3 16.66667 3.333333 5.000000e+00
M4 16.66667 3.333333 5.000000e+00
M5 0.00000 0.000000 0.000000e+00
M6 0.00000 0.000000 0.000000e+00
M7 16.66667 3.333333 5.000000e+00
M8 16.66667 3.333333 5.000000e+00
> sessionInfo()
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] FactoMineR_1.09
>
Steven McKinney wrote:
>
>
> Not likely that anyone can explain, as
> there is not enough information in your
> email.
>
> Including the contents of the freqtest.txt file
> was a good idea, as the posting guide suggests
> (the posting guide is that clearly labeled bit
> at the bottom that looks like this:
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> Check it out! It is cool.)
>
> Additionally, include the command
> sessionInfo()
> and its output from all machines you refer to
> so maintainers know which versions of software
> you are running. Also, include the output you obtained
> from your code (with your code being a self-contained
> and reproducible set of R commands).
>
> Finally, describe what the difference is and why
> the difference is problematic (i.e. don't report
> machine precision differences, or sign differences
> for PCA results - PCA vector directions are arbitrary
> modulo 180 degrees).
>
>> I also tried mean(xrcc2) and sd(xrcc2) on both machines, the results are
>> the
>> same.
>> Please explain.
>
> The R maintainers do an amazing job of creating
> numerically stable platform-independent software,
> so you get the same results almost everywhere.
> (Thank you R core!)
>
>
> HTH
>
> Steve McKinney
>
> -----Original Message-----
> From: r-help-bounces at r-project.org on behalf of jathine
> Sent: Tue 9/16/2008 2:19 PM
> To: r-help at r-project.org
> Subject: [R] Different PCA results under Windows and Linux
>
>
> I ran the following R script under both Linux and Windows, and got 2
> different results.
> Linux R version 2.7.1 and Windows R version 2.7.2.
>
>> library(FactoMineR)
>>x1=read.table("freqtest.txt",header=TRUE)
>>xrcc2=x1[,1:8]
>>p1=PCA(xrcc2, graph=FALSE)
>>p1$var
>
> freqtest.txt file lines of text :
> M1 M2 M3 M4 M5 M6 M7 M8
> -1 -1 -1 -1 -1 -1 -1 -1
> 0 0 0 0 -1 -1 1 1
> -1 -1 -1 -1 -1 -1 -1 -1
> 0 0 0 0 -1 -1 1 1
>
> I also tried mean(xrcc2) and sd(xrcc2) on both machines, the results are
> the
> same.
> Please explain.
>
>
> --
> View this message in context:
> http://www.nabble.com/Different-PCA-results-under-Windows-and-Linux-tp19520449p19520449.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at 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
> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at 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
> and provide commented, minimal, self-contained, reproducible code.
>
>
--
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