Search
Question: Cannot load old SummarizedExperiment in R 3.3, Bioc 3.3
0
gravatar for Ryan C. Thompson
17 months ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson6.1k 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: https://www.dropbox.com/s/5d3vktytsb0b22x/promoter-group-counts-1kb.RDS?dl=0

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

ADD COMMENTlink modified 17 months ago by Hervé Pagès ♦♦ 13k • written 17 months ago by Ryan C. Thompson6.1k
2
gravatar for Hervé Pagès
17 months 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.

Thanks,

H.

ADD COMMENTlink written 17 months ago by Hervé Pagès ♦♦ 13k

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

ADD REPLYlink written 17 months ago by Ryan C. Thompson6.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 269 users visited in the last hour