error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
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mathai.c • 0
@mathaic-22456
Last seen 3.3 years ago
library(SingleR)
hpca.se <- HumanPrimaryCellAtlasData()
hpca.se
library(scRNAseq)
hESCs <- LaMannoBrainData('human-es')
hESCs <- hESCs[,1:100]

# Restrict to common genes between test and reference data:
library(scater)
common <- intersect(rownames( hESCs ), rownames( hpca.se ))
hpca.se <- hpca.se[common,]
hESCs <- hESCs[common,]
hESCs <- logNormCounts(hESCs)

Error in (function (classes, fdef, mtable)  :    unable to find an inherited method for function ‘logNormCounts’ for signature ‘"Seurat"’


Can someone help me why im getting this error?

seurat singleR • 2.1k views
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I added formatting to your post so that it is readable. Also note that you are asking a question rather than providing a tutorial.

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Aaron Lun ★ 28k
@alun
Last seen 6 hours ago
The city by the bay

Usually it's good form to format your post correctly with, y'know, new lines and stuff.

Moreover, Seurat is not a Bioconductor package, and none of the packages you show use Seurat. I am confident in saying that none of the code as shown above will generate a Seurat object at any point.

I will conclude by identifying the code as originating from the SingleR vignette, though you haven't copy-and-pasted it correctly or completely, e.g., rownameshpca.se).

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in the case of row nameshpcs.se) I did put the brackets, somehow its not displayed in this