[BioC] Problem running summarizeOverlaps()

[Jessica Perry Hekman]

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


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



-- 
Jessica P. Hekman, DVM, MS
PhD student, University of Illinois, Urbana-Champaign
Animal Sciences / Genetics, Genomics, and Bioinformatics