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satijalab / azimuth

A Shiny web app for mapping datasets using Seurat v4
https://satijalab.org/azimuth
GNU General Public License v3.0
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"SCT is not an assay present in the given object" even though it is present #183

Open viktorfeketa opened 11 months ago

viktorfeketa commented 11 months ago

When running Azimuth while specifying assay = "SCT"

I am getting an error: Error in GetAssay.Seurat(object = object, assay = assay) : SCT is not an assay present in the given object. Available assays are: RNA

even though the query Seurat object clearly contains the "SCT" assay

I am using a custom-made Azimuth reference produced from a public dataset using AzimuthReference() with specifying: refAssay = "SCT" so the reference assay should also contain the SCT assay

Gesmira commented 10 months ago

Can you include the output of query@assays ?

viktorfeketa commented 10 months ago

sure, here it is:

> srInt@assays
$RNA
Assay data with 18474 features for 253099 cells
First 10 features:
 NOSTRIN, CERS6, STK39, LYPD6, FIGN, LYPD6B, KCNH7, KIF5C, DAPL1, GCA 

$SCT
SCTAssay data with 16941 features for 253099 cells, and 15 SCTModel(s) 
First 10 features:
 NOSTRIN, CERS6, STK39, LYPD6, FIGN, LYPD6B, KCNH7, KIF5C, DAPL1, GCA 

$integrated
SCTAssay data with 3000 features for 253099 cells, and 1 SCTModel(s) 
Top 10 variable features:
 NPY, APOD, C1QA, PTGDS, SST, DCN, CARTPT, POMC, AGRP, PLP1
erzakiev commented 7 months ago

I think the topic starter should have just used the integrated assay and it would have probably solved his issue...