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SingleR-inc / celldex

Collection of cell type reference datasets.
https://bioconductor.org/packages/devel/data/experiment/html/celldex.html
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HumanPrimaryCellAtlasDAta() - invalid class "SummarizedExperiment" object #17

Closed LineS97 closed 2 years ago

LineS97 commented 2 years ago

Hi!

Today, I experienced this issue:

image

I have been following the vignette: https://rdrr.io/github/LTLA/celldex/f/vignettes/userguide.Rmd

library(celldex) ref <- HumanPrimaryCellAtlasData()

I get the following error: snapshotDate(): 2022-04-26 see ?celldex and browseVignettes('celldex') for documentation loading from cache see ?celldex and browseVignettes('celldex') for documentation loading from cache Error in validObject(.Object) : invalid class “SummarizedExperiment” object: nb of cols in 'assay' (2) must equal nb of rows in 'colData' (713)

Versions: celldex_1.6.0 SummarizedExperiment_1.26.1 R version 4.2.0

LTLA commented 2 years ago

I think your cache is corrupted. Perhaps you can try forcing an update with:

ExperimentHub::ExperimentHub()[["EH3492", force=TRUE]]

And then running HumanPrimaryCellAtlasData() again.

LineS97 commented 2 years ago

It solved my problem! Thank you!

gadepallivs commented 1 year ago

I'm trying to automatically add cell indents for https://www.heartcellatlas.org/. If I use, HumanPrimaryCellAtlasData() , get too many indents assigned and overlap. How to filter uses only relevant heart cells ?