[R] principal component analysis in affy
Adaikalavan Ramasamy
ramasamy at cancer.org.uk
Fri Jul 22 01:15:59 CEST 2005
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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