From: Wagle, Mugdha <Mugdha.Wagle_at_STJUDE.ORG>

Date: Fri 22 Jul 2005 - 01:09:50 EST

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R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jul 22 01:46:48 2005

Date: Fri 22 Jul 2005 - 01:09:50 EST

Hi,

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

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jul 22 01:46:48 2005

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