Question: Help with the output from mnnCorrect
0
gravatar for sharvari gujja
5 weeks ago by
United States
sharvari gujja20 wrote:

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 • 74 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by sharvari gujja20

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 REPLYlink written 4 weeks ago by Steve Lianoglou12k

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 REPLYlink written 4 weeks ago by Aaron Lun25k
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