[BioC] GenePlotter - new user question

[Chris Doucette]

Hi,

I've just recently started using the bioconductor packages. I'm trying to
set up the example script for "Whole Genome Plotting" in the help file
called visualize.pdf (I'll paste it in at the end of the message). When
the script runs in R, I notice three differences between the image that's
generated and the sample image in the PDF:

1) The lengths of the chromosomes are nearly uniform, whereas they vary
greatly in the PDF (the Y chromosome is almost as long as chromosome 1!)

2) Only 8 or so genes are colored in by cColor, whereas there are a few
hundred colored genes in the PDF

3) The script generates "50 or more" (apparently 50 is the limit) warnings
which all say the same thing:

the condition has length > 1 and only the first element will be used in:
if (is.na(y)) y else names(y)


I'm somewhat unfamiliar with R and I'm entirely in the dark as to what's
causing the problem. One person suggested that the data package (hgu95av2)
might have corrupted data. I've tried other packages from the website and
the same thing happens.

I have been able to track the source of the warnings to the call to
chrObj <- buildChromLocation("hgu95av2"). I'm still not sure what it means
or what effect it's having on the results.

Here's the script I'm trying to run (copied verbatim from the PDF):


library(geneplotter)
data(eset)
mytt <- function(y) {
ys <- split(y, cov2)
t.test(ys[[1]], ys[[2]])
}
ttout <- esApply(eset, 1, mytt)
s1means <- sapply(ttout, function(x) x$estimate[1])
s2means <- sapply(ttout, function(x) x$estimate[2])
deciles <- quantile(c(s1means, s2means), probs = seq(0, 1, 0.1))
s1class <- cut(s1means, deciles)
names(s1class) <- names(s1means)
s2class <- cut(s2means, deciles)
names(s2class) <- names(s2means)

cols <- dChip.colors(10)
nf <- layout(matrix(1:3,nr=1), widths=c(5,5,2))
chrObj <- buildChromLocation("hgu95av2")
cPlot(chrObj)
cColor(geneNames(eset), cols[s1class], chrObj)
cPlot(chrObj)
cColor(geneNames(eset), cols[s2class], chrObj)
image(1,1:10,matrix(1:10,nc=10),col=cols, axes=FALSE,
xlab="", ylab="")
axis(2, at=(1:10), labels=levels(s1class), las=1)


Has anyone experienced a similar issue trying to run this script? Is there
an updated version of the packages I should download? (I ran the
installation yesterday using "Install from Bioconductor site" so
theoretically the latest versions should all be there...)

Thanks,
- Chris Doucette
doucett at fas.harvard.edu