R help - Jul 2005 - principal component analysis in affy

Hi,
 
I have been using the prcomp function to perform PCA on my example microarray
data, (stored in metric text files) which looks like this:
 
        1a 1b 1c 1d 1e 1f ...................................................4r
4s 4t
g1    1.2705 1.2766
...........................................................2.0298
g2    0.1631
........................................................................0.7067
g3    0.2212
........................................................................1.0439
.
.
.
.
g99 
1.3657..........................................................................2.3736
 
i.e. a matrix of 63 columns and 99 rows, where the columns represent chip and
rows represent genes. Now, the biplot function
 
biplot(prcomp(pcadata, scale = TRUE), cex = c(0.75,0.75))
 
gives me a plot with one vector per gene. However, I actually need to get one
vector per chip instead of one vector per gene.  I have been told that there is
a function in the affy package that does what I am looking for i.e. gives one
vector per chip. Can someone please tell me what the function is called, and how
I can get hold of the code(since I believe affy only works on CEL files) ? I
have downloaded the affy R code from Terry Speed's website already, but I
don't know where (if at all) the code to perform PCA is.
 
Thank you everyone!
 
Sincerely,
Mugdha Wagle
Hartwell Center for Bioinformatics and Biotechnology,
St.Jude Children's Research Hospital, Memphis TN 38105

1) Please learn to wrap your emails to 72 characters per line. See 
http://expita.com/nomime.html

2) You might have better luck with the BioConductor folks. Their mailing
list is https://stat.ethz.ch/mailman/listinfo/bioconductor

3) The affy package has many functions including some algorithms for
preprocessing CEL files.

4) I do not understand why you need the affy package if you do not have
CEL files ? I presume that you only have a subset of the final data.

5) I do not understand your question but you might want to simply
transpose the matrix before doing a prcomp() on it. See help("t").

Regards, Adai



On Thu, 2005-07-21 at 10:09 -0500, Wagle, Mugdha wrote:
> Hi,
>  
> I have been using the prcomp function to perform PCA on my example
microarray data, (stored in metric text files) which looks like this:
>  
>         1a 1b 1c 1d 1e 1f
...................................................4r 4s 4t
> g1    1.2705 1.2766
...........................................................2.0298
> g2    0.1631
........................................................................0.7067
> g3    0.2212
........................................................................1.0439
> .
> .
> .
> .
> g99 
1.3657..........................................................................2.3736
>  
> i.e. a matrix of 63 columns and 99 rows, where the columns represent chip
and rows represent genes. Now, the biplot function
>  
> biplot(prcomp(pcadata, scale = TRUE), cex = c(0.75,0.75))
>  
> gives me a plot with one vector per gene. However, I actually need to get
one vector per chip instead of one vector per gene.  I have been told that there
is a function in the affy package that does what I am looking for i.e. gives one
vector per chip. Can someone please tell me what the function is called, and how
I can get hold of the code(since I believe affy only works on CEL files) ? I
have downloaded the affy R code from Terry Speed's website already, but I
don't know where (if at all) the code to perform PCA is.
>  
> Thank you everyone!
>  
> Sincerely,
> Mugdha Wagle
> Hartwell Center for Bioinformatics and Biotechnology,
> St.Jude Children's Research Hospital, Memphis TN 38105
> 
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