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July 07, 2009

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They don't provide the source data, otherwise I'd give it a shot.

Someone named "andersduck" took a shot at it -- I don't know if the URL they read was the same as the one in the examples ...

###################
## yes R is very nice. The code (without using any specific ## expression data package) is very fast to write:

## read data
dat<-read.delim("http://www.bme.utexas.edu/research/orly/GSVD/data/Yeast.txt",skip=1,as.is=TRUE,na="Null")

## barplot of missing
barplot(table(apply(is.na(dat[,-(1:6)]),1,sum)),col=2,ylab="Number of genes",xlab="Number of controls")

## remove arrays with missing data
dat<-dat[!apply(is.na(dat[,-(1:6)]),1,any),]

## Calculate SVD
s<-svd(dat[-(1:6)])

## Plot barchart
barplot(s$d^2/sum(s$d^2))

## plot two first eigengenes
lattice::dotplot(s$v[,1:2])

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