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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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CreateSinglerObject Error #110

Open KBoostan opened 4 years ago

KBoostan commented 4 years ago

Hi Dvir, I'm trying to annotate cells from a dataset of lung tumor cells and healthy tumor cells that I merged together. I can't figure out where I am making a mistake. I have pre-processed, normalized, and run linearly reduction on the data, which worked just fine, but when I get to SingleR, I get this error:

singler = CreateSinglerObject(counts = lung.combined3, annot = NULL, project.name="analysis", min.genes = 0, technology = "10X", species = "Human", citation = "", ref.list = list(lung.combined3), normalize.gene.length = F, variable.genes = "de", fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = T, reduce.file.size = T, numCores = SingleR.numCores)

Error in dimnames(x) <- dn : 'dimnames' applied to non-array Thank you for your help! Kaveh

dviraran commented 4 years ago

Hi,

I guess its because of ref.list = list(lung.combined3) which is supposed to be the reference object, not the counts data (you can omit it completely if using the regular references). Anyhow, please try our new version, now in Bioconductor - https://bioconductor.org/packages/devel/bioc/html/SingleR.html. Hopefully, the workflow and the documentation is clearer there.

Best, Dvir