Help with the output from mnnCorrect

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sharvari gujja ▴ 40

@sharvari-gujja-6614

Last seen 22 months ago

United States

Hi,

I am trying to use mnnCorrect to identify shared cell population between two batches from different conditions - WT and KO.

classic.out <- batchelor::mnnCorrect(sce1, sce2, subset.row=chosen.hvgs , correct.all = TRUE)

Using HVGs as input to mnnCorrect function, I get:

 > classic.out
class: SingleCellExperiment 
dim: 9608 2542 
metadata(1): merge.info
assays(1): corrected
rownames(9608): ENSMUSG00000000056.7 ENSMUSG00000000078.7 ... NA NA
Error in `rownames<-`(`*tmp*`, value = c("ENSMUSG00000000056.7", "ENSMUSG00000000078.7",  : 
  missing values not allowed in rownames

There are no NAs in the individual single cell objects. Can you please help with the error.

Thanks

mnnCorect MNN • 1.1k views

ADD COMMENT • link 5.2 years ago sharvari gujja ▴ 40

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Do all of the values in chosen.hvgs appear in both rownames(sce1) and rownames(sce2)?

Which is to say, the output of this operation should be empty:

setdiff(chosen.hvgs, intersect(rownames(sce1), rownames(sce2)))

is it?

ADD REPLY • link 5.2 years ago Steve Lianoglou ★ 13k

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In the future, it would help to tag this question with the relevant package name, i.e., batchelor. Otherwise the maintainer (i.e., me) will not even see it.

ADD REPLY • link 5.2 years ago Aaron Lun ★ 28k

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