hello,

How many genes or exons do you have per chromosome?  If you have 35 
genes, but these are all on different chromosomes, then the package is 
probably not appropriate.  The package relies on the ability to observe 
deviations from the expected read depth along thousands of observations, 
where each chromosome is fit separately.  for example, if you have a 
single gene targeted on a chromosome, and in one sample a duplication 
overlaps all the exons of this gene, there is no chance to recover this 
event.

If it is possible to email me the subset of data that produced the 
error, I can try to see what happened:

save(rdata["Chr10"], file="rdata_subset.RData")

best,

Mike

On 12/18/2012 05:19 PM, Mike Love wrote:
>
>
> ---------- Forwarded message ----------
> From: *nat [guest]* <guest@bioconductor.org 
> <mailto:guest@bioconductor.org>>
> Date: Tue, Dec 18, 2012 at 5:04 PM
> Subject: [BioC] ExomeCopy package error
> To: bioconductor@r-project.org <mailto:bioconductor@r-project.org>, 
> nconte@ebi.ac.uk <mailto:nconte@ebi.ac.uk>
>
>
>
> Hi,
> I am testing ExomeCopy on a set of illumina sequencing data generated 
> after agilent custum gene set  capture, only  35 gene exons overall (~ 
> 300 Mb total).
> 1-My first question would be : is the method reliable for smaller capture?
> 2-Secondly.,
> I sucessfully used  the method on the data provided with the vignette. 
> I then tried with my own set of data
> in total 10 samples, across  2282 rows , I have  calculated the GC and 
> bg values nad went on to the next step where I ran exomeCopy on one 
> sample and one chromosome
>
> ###this seems to work for certains samples, expect the warning for 
> small subset
> > fit <- exomeCopy(rdata["Chr10"], sample.name <http://sample.name> = 
> exome.samples[10],
> + X.names = c("bg", "GC", "GC.sq", "width"), S = 0:6,
> + d = 2)
> Warning message:
> In exomeCopy(rdata["Chr10"], sample.name <http://sample.name> = 
> exome.samples[10], X.names = c("bg",  :
>   exomeCopy was tested for thousands of ranges covering a targeted 
> region on a single chromosome.  The results might not be reliable for 
> less than a hundred ranges.
>
>
> ###then I try with another sample and got this error message
> Error in if (goto.cnv < 1/(nstates - 1)) { :
>   missing value where TRUE/FALSE needed
>
> I am not sure where this comes from and would like some help on this
>
> >  fit <- exomeCopy(rdata["Chr10"], sample.name <http://sample.name> = 
> exome.samples[7],
> + X.names = c("bg", "GC", "GC.sq", "width"), S = 0:6,
> + d = 2)
> Error in if (goto.cnv < 1/(nstates - 1)) { :
>   missing value where TRUE/FALSE needed
> In addition: Warning message:
> In exomeCopy(rdata["Chr10"], sample.name <http://sample.name> = 
> exome.samples[7], X.names = c("bg",  :
>   exomeCopy was tested for thousands of ranges covering a targeted 
> region on a single chromosome.  The results might not be reliable for 
> less than a hundred ranges.
> > exome.samples
>  [1] "sample9"  "sample8"  "sample7"  "sample6"  "sample5"  "sample1"
>  [7] "sample16" "sample15" "sample14" "sample13"
>
>
> example if my data
>
> #####
> RangedData with 2282 rows and 15 value columns across 18 spaces
>         space                 ranges   |   sample9   sample8 sample7
>      <factor>              <IRanges>   | <integer> <integer> <integer>
> 1        Chr1 [115247069, 115247168]   |      4369      4446    3675
> 2        Chr1 [115247169, 115247268]   |      8222      8081    6978
> 3        Chr1 [115247269, 115247368]   |      9548     10026    8690
>
>  -- output of sessionInfo():
>
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=C
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] exomeCopy_1.2.0      Rsamtools_1.8.6  Biostrings_2.24.1
> [4] GenomicRanges_1.8.13 IRanges_1.14.4 BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-4.1 stats4_2.15.0  tools_2.15.0 zlibbioc_1.2.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org 
> <http://bioconductor.org>.
>
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