Question: error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
0
gravatar for mathai.c
16 days ago by
mathai.c0
mathai.c0 wrote:
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 • 135 views
ADD COMMENTlink modified 12 days ago by Gordon Smyth39k • written 16 days ago by mathai.c0

I added formatting to your post so that it is readable. Also note that you are asking a question rather than providing a tutorial.

ADD REPLYlink modified 16 days ago • written 16 days ago by Gordon Smyth39k
Answer: error in (function (classes, fdef, mtable) unable to find an inherited method f
0
gravatar for Aaron Lun
16 days ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

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).

ADD COMMENTlink written 16 days ago by Aaron Lun25k

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

ADD REPLYlink written 12 days ago by mathai.c0
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