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Error when running ```restrictCorpus```

Open cathalgking opened this issue 4 months ago • 2 comments

I encounter the error below when running restrictCorpus on a 10x Visium dataset (TMA) contained within a SpatialFeatureExperiment object. Can you advise how to get past this?

vis1 <- restrictCorpus(cd, removeAbove=1.0, removeBelow = 0.05, nTopOD = 1000)

Removing 0 genes present in 100% or more of pixels...
18085 genes remaining...
Removing 5615 genes present in 5% or less of pixels...
12470 genes remaining...
Restricting to overdispersed genes with alpha = 0.05...
Converting to sparse matrix ...
Calculating variance fit ...
Using lm ...
Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

data

vis1
class: SpatialFeatureExperiment 
dim: 18085 5210 
metadata(0):
assays(1): counts
rownames(18085): SAMD11 NOC2L ... MT-ND6 MT-CYB
rowData names(8): symbol Feature.Type ... Median.Normalized.Average.Counts_sample01 Barcodes.Detected.per.Feature_sample01
colnames(5210): AACAATCCGAGTGGAC-1 AACACCAGCCTACTCG-1 ... TGTTGGTGCGGAATCA-1 TGTTGGTGGACTCAGG-1
colData names(4): in_tissue array_row array_col sample_id
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
imgData names(4): sample_id image_id data scaleFactor

unit: full_res_image_pixel
Geometries:
colGeometries: spotPoly (POLYGON) 

Graphs:
sample01: col: visium

cathalgking avatar Aug 27 '25 09:08 cathalgking