[Bioc-sig-seq] Error while trying to xyplot. Perhaps a lattice problem.

[ig2ar-saf2 at yahoo.co.uk]

Hello everybody,

I am working with the yet unreleased package chipseq.

There is a very nice xyplot that I am trying to reproduce from the

http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/ChipSeqWorkflow.pdf

However, R complains saying

"Error in limits.and.aspect(prepanel.default.xyplot, prepanel = prepanel,  : 
need at least one panel"

What am I doing? This

> class(E1)
[1] "GenomeDataList"
attr(,"package")
[1] "BSgenome"
> names(E1)
[1] "C1" "C2" "T1" "T2"
> islandReadSummary <- function(x)
+ {
+ g <- extendReads(x, seqLen = 200)
+ s <- slice(coverage(g, 1, max(end(g))), lower = 1)
+ tab <- table(viewSums(s) / 200)
+ ans <- data.frame(nread = as.numeric(names(tab)), count = as.numeric(tab))
+ ans
+ }
> nread.islands <- as(gdApply(E1, islandReadSummary), "data.frame")
There were 50 or more warnings (use warnings() to see the first 50)
> xyplot(log(count) ~ nread | sample,
+        nread.islands,
+        subset = (chromosome == "chr19" & nread <= 40),
+        layout = c(1, 4), pch = 16, type = c("p", "g"))
Error in limits.and.aspect(prepanel.default.xyplot, prepanel = prepanel,  : 
  need at least one panel
> 

Can anybody shed some light?

Clarification: the warning "There were 50 or more warnings (use warnings() to see the first 50)" comes from IRanges. chipseq is using the slightly older start/end convention rather than the newer shift/step convention.

Thank you,

Ivan