I am following RNA-seq workflow (http://www.bioconductor.org/help/workflows/rnaseqGene/) using my data and I am trying to get read counts using summarizeOverlaps function. Unfortunately, it is impossible because of this error:
error 'validObject(.Object)': invalid class “SummarizedExperiment” object: 'rowRanges' length differs from 'assays' nrow
I am able to prepare read counts table only for one chromosome (e.g. seqlevels(txdb,force=TRUE)<-seqlevels(txdb)), but when I want to do this for more chromosomes (1, 2, ..., 22, X and Y) seqlevels(txdb,force=TRUE)<-seqlevels(txdb)[1:24] I get mentioned error.
Any idea why?
My second problem is with function register(MulticoreParam(workers = 2)) (BiocParallel package). Not always, but very often I get error 'unserialize(socklist[[n]])'. Do you know why or what I can do to avoid this error?