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carmonalab / STACAS

R package for semi-supervised single-cell data integration
GNU General Public License v3.0
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Run.STACAS Error in GetAssayData #28

Closed gianfilippo closed 1 year ago

gianfilippo commented 1 year ago

Hi,

I am trying STACAS on my 12 samples Seurat data obj, scdata.Each sample is preprocessed (i.e. QCd, filtered and normalized). The range for the N of cells in the samples is [245, 8958]. The range for the N of features in the RNA assay in the samples is [16900, 27554]

When I try to integrate using scdata.combined <- Run.STACAS(scdata, dims = 1:nPCs, anchor.features = intfeatures, new.assay.name = "stacas") where intfeatures results from SelectIntegrationFeatures and is a vector of ~3000 elements

I get the following error : Integrating dataset 4 with reference dataset Error in GetAssayData(object = object, assay = umi.assay, slot = "counts")[features_to_compute, : no 'dimnames' attribute for array

Same error if I set anchor.features = 3000

As far as I understand this probably is because the AssayData is an empty matrix, which I assume it is because features_to_compute may be an empty vector.

I am not sure why this is happening. o you have any suggestions ?

Thanks

gianfilippo commented 1 year ago

Sorry, my fault. The wrong assay was selected.....