[BioC] Problem running summarizeOverlaps()

[Martin Morgan]

On 05/19/2014 06:55 PM, Jessica Perry Hekman wrote:
> I am working from
>
> http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf
>
>
> Before writing my own script, I attempted to run the exact code from that vignette:
>
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> exByGn <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, "gene")
>
> # Read counts
> library(Rsamtools)
> fls <- list.files("../../bam/", pattern="fox-readgroups.bam$", full.names=T)
>
> library(leeBamViews)  # I inserted this line
> bamfls <- BamFileList(fls)
>
> flag <- scanBamFlag(isNotPrimaryRead=FALSE, isProperPair=TRUE)
> param <- ScanBamParam(flag=flag)
> gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
>           ignore.strand=TRUE, single.end=TRUE, param=param)
> hnrnp.cnts=assay(gnCnt)
>
>
> When I executed this in R, I got the error message on the second to last line:
>
> Error in validObject(.Object) :
>    invalid class “SummarizedExperiment” object: 'rowData' length differs from
> 'assays' nrow
> In addition: Warning message:
> In lapply(setNames(seq_along(reads), names(reads)), function(i,  :
>    all scheduled cores encountered errors in user code

Hi Jessica --

I think that summarizeOverlaps is trying to evaluate your counting algorithm in 
on several different cores, but an error occurs. Try running the commands above, 
and then immediately before summarizeOverlaps evaluate

   options(mc.cores=1)
   gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
       ignore.strand=TRUE, single.end=TRUE, param=param)

Hopefully this will at least make the error apparent, even if it might still be 
cryptic.

Please be sure to include the output of the command 'sessionInfo()' after you 
have a problem; here's mine

 > sessionInfo()
R version 3.0.2 Patched (2014-01-02 r64626)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Rsamtools_1.14.3     Biostrings_2.30.1    GenomicRanges_1.14.4
[4] XVector_0.2.0        IRanges_1.20.7       BiocGenerics_0.8.0
[7] BiocInstaller_1.12.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6   stats4_3.0.2   zlibbioc_1.8.0

(actually, this is my best guess at the version of R you're using; there's a 
more recent version, and more recent versions of the packages, available).

Hope that helps,

Martin

>
>
> I'm not sure what to make of this error message. Apparently SummarizedExperiment
> is the output object which I should be getting back from summarizeOverlaps(). Is
> this a problem with the data I'm putting in? (But it is just the example data
> used in the vignette, so it should be trustworthy.)
>
> Any suggestions welcome!
>
> Thanks,
> Jessica
>
>
>


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