[BioC] PCA-prcomp() versus plotPCA

[James W. MacDonald]

Hi Marco,

That sounds reasonable. I will add this functionality to the devel 
version of affycoretools, probably this week. You don't mention your OS, 
but if you are on Windows I might need to send you a binary, as the 
binary affycoretools tends not to get built until close to release time 
(because it depends on biomaRt, which depends on RCurl, which takes a 
bit of work to build on windows...).

Best,

Jim

marco fabbri wrote:
> Hi James,
>  thank you for the quick reply.
> More than plot all the three PCs, I would like to decide which two to
> plot, for example to plot PC2 versus PC3.
> If you are implementing please let me know I will use for sure.
> 
> Marco
> 
> On 14/11/06, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> 
>> Hi Marco,
>>
>> marco fabbri wrote:
>> > Two question on PCA:
>> >
>> > 1. I like plotPCA from affycoretools package, but I was not able to
>> > plot the third component.
>> > Am I wrong?
>>
>> No you are not wrong. By default plotPCA() only does the first two
>> principal components. If there is interest I could easily add the
>> capability to do the first three PCs and plot using scatterplot3D.
>>
>> >
>> > 2.I try the prcomp() function and  I compared it to plotPCA.
>> >
>> > TesetA=t(exprs(esetA))
>> > pca=prcomp(TAM,  retx=TRUE,center=TRUE, scale= TRUE)
>> > plot(pca$x[,1:2])
>> > --------
>> > plotPCA(esetA,groups=c(1:10))
>> >
>> > I had different plots.
>> > Can please help me to understand better what  plotPCA is doing?
>>
>> plotPCA() is using the default arguments to prcomp(), which includes
>> scale.=FALSE. Usually one wants to scale data prior to performing the
>> PCA if the data are on different scales. However, most Affy data are
>> normalized which should put the data on similar scales, so I just stick
>> with the default.
>>
>>
>> HTH,
>>
>> Jim
>>
>>
>> >
>> >
>> > Thank you
>> > MArco
>> >
>>
>>
>> -- 
>> James W. MacDonald, M.S.
>> Biostatistician
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
>> 734-647-5623
>>
>>
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should 
>> not be used for urgent or sensitive issues.
>>
> 
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.