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

[Laurent Gautier]

On Tue, 2009-04-28 at 16:58 +0000, ig2ar-saf2 at yahoo.co.uk wrote:
> 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?

What does return the command below ?
str(subset(nread.islands, chromosome == "chr19" & nread <= 40))


> 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
> 
> 
> 
> 
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