[R] principal component analysis in affy
Wagle, Mugdha
Mugdha.Wagle at STJUDE.ORG
Thu Jul 21 17:09:50 CEST 2005
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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