BiocParallel errors

[antoine4ucsd]

Hello I am eager to try SingleR to identify cell subset from scRNAseq data. I followed this tutorial https://bioconductor.org/packages/devel/bioc/vignettes/SingleR/inst/doc/SingleR.html but I get an unusual error:

library(SingleR)
pred.hesc <- SingleR(test = hESCs, ref = hpca.se, assay.type.test=1,
    labels = hpca.se$label.main)

gives me:

Error: BiocParallel errors
  1 remote errors, element index: 1
  2 unevaluated and other errors
  first remote error:
Error: BiocParallel errors
  0 remote errors, element index: 
  25 unevaluated and other errors
  first remote error:

I am using a Mac (last gen)

thank you!

[LTLA]

Nothing obvious comes to mind. I just ran it on my own computer and it works fine. Make sure you're using the latest version of all packages (i.e., using BioC 3.16, no issues from BiocManager::valid()).

[antoine4ucsd]

thank you. I figured it may be a Mac issue . I have BioC 3.15 installed. I will update it I am attaching my session info if you can find anything else obvious

session info.txt

[antoine4ucsd]

Also if I may I am trying to identify human brain cells (microglia, astrocyte, neurons, dendritic cells, etc) that are also likely mixed with endothelial cells and probably T cells and some other immune cells. If I use the BlueprintEncodeData ref alone or combined with HumanPrimaryCellAtlasData, I mostly recover monocytes but NO microglial cells.... is there a better combined atlas to use for such samples? I also try clustifyr package and it find mostly microglial cells... Such different results are intriguing.

I just ran

[antoine4ucsd]

and great news. It finally worked after updating to BioC 3.16 and all related packages... I am still unsure why all cells are identified as mostly monocytes since they are predominiantly microglial cells. if you could advise on the best combined atlas to build, that would be great!

ref <- BlueprintEncodeData()
pred <- SingleR::SingleR(test=mydata, ref=ref, labels=ref$label.main)

resulting in:

   Adipocytes           B-cells      CD8+ T-cells                DC Endothelial cells      Erythrocytes       Fibroblasts 
                8                 8                 2               416                62                 9                 1 
              HSC       Macrophages         Monocytes       Neutrophils          NK cells 
                2               553              1068                 2                 4 

[LTLA]

Neither of those two references have "microglia", so it's not a surprise that they aren't found.

I don't have much experience with neuronal references, but you could probably make your own from the classic scRNAseq::ZeiselBrainData. You should be able to do something like:

zeisel <- scRNAseq::ZeiselBrainData()
zeisel <- scuttle::logNormCounts(zeisel)
ref <- aggregateReference(zeisel, zeisel$level1class) # or level2class

and then use that as a reference. Possibly you would want to throw in BlueprintEncode as another reference (see here), as the Zeisel dataset doesn't contain any coverage for immune types.

[antoine4ucsd]

I will give it a try and let you know how it works! Much appreciated.

[antoine4ucsd]

still not what I would expect. mostly pyramidal CA1 (?) I will keep looking for other sources but all advices are welcome.

astrocytes_ependymal    endothelial-mural            microglia        pyramidal CA1 
                  35                    5                   98                 1997 

[LTLA]

I'd suggest that you look into some of the diagnostics, e.g., here.

[antoine4ucsd]

on it thank you for being so responsive.

[antoine4ucsd]

It works well with a new combined ref DarmanisBrainData and HumanPrimaryCellAtlasData thank you again for your assistance.

[Roner2022]

hello， I am eager to try SingleR to identify cell subset from scRNAseq data.

cellpred <- SingleR(test = testdata,
ref = refdata, labels = refdata$label.main, method = "cluster", clusters = clusters, assay.type.test = "logcounts", assay.type.ref = "logcounts") but I get an unusual error: Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error in .read_block_OLD(x, viewport, as.sparse = as.sparse): could not find function ".read_block_OLD"

window10

[LTLA]

Make a new issue, don't keep reviving old threads.