[R] principal component analysis in affy

From: Wagle, Mugdha <Mugdha.Wagle_at_STJUDE.ORG>
Date: Fri 22 Jul 2005 - 01:09:50 EST


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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