Question: Cannot load old SummarizedExperiment in R 3.3, Bioc 3.3
gravatar for Ryan C. Thompson
2.5 years ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson7.1k wrote:

I have some SummarizedExperiment objects from previous Bioconductor and R versions, and I've been using them in subsequent analyses by running updateObject() on them. However, after updating to R 3.3, I now get the following when I try to do so:

> sexp <- readRDS("promoter-group-counts-1kb.RDS") %>% updateObject
Error in validObject(result) :
  invalid class "SummarizedExperiment" object:
  nb of rows in 'assay' (35631) must equal nb of rows in 'rowData' (0)
In addition: Warning message:
In updateObjectFromSlots(object, ..., verbose = verbose) :
  dropping slot(s) 'rowData', 'exptData' from object = 'SummarizedExperiment'

I don't remember exactly what version of Bioc these were generated under, but I know it was before the introduction of RangedSummarizedExperiment. In any case, you can access the file here:

Can anyone help me figure out how to load this data into the new BioC version?

ADD COMMENTlink modified 2.5 years ago by Hervé Pagès ♦♦ 13k • written 2.5 years ago by Ryan C. Thompson7.1k
gravatar for Hervé Pagès
2.5 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi Ryan,

The "updateObject" method for SummarizedExperiment was removed in BioC 3.3. It seems that it was a little bit too early for that, sorry. Note that updateObject() is typically a one-time use i.e. one should normally re-serialize the object after running updateObject() on it. That way all the old serialized SummarizedExperiment objects hanging around get replaced by new ones little by little.

I restored the "updateObject" method in SummarizedExperiment 1.2.3 (release) and 1.3.4 (devel). Please use it to fix and re-serialize your old SummarizedExperiment objects.



ADD COMMENTlink written 2.5 years ago by Hervé Pagès ♦♦ 13k

Thanks. Good to know. I'll update all my SummarizedExperiment objects and re-serialize them.

ADD REPLYlink written 2.5 years ago by Ryan C. Thompson7.1k
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