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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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doScrubletDetect Function Error #523

Open annaminyifeng opened 1 year ago

annaminyifeng commented 1 year ago

Hello,

I tried to run the function doScrubletDetect after creating my Giotto object but I am running into this error:

Error in as.vector(data) : no method for coercing this S4 class to a vector

Please let me know if there is a solution to fix this error.

jiajic commented 1 year ago

Hi @annaminyifeng

Could you try again after updating?

Best, Jiaji

annaminyifeng commented 1 year ago

Hi @jiajic

I tried again after updating but now I get a new error.

caught segfault address (nil), cause 'unknown'

Traceback: 1: py_call_impl(callable, dots$args, dots$keywords) 2: python_scrublet(counts_matrix = scr_input, expected_doublet_rate = expected_doublet_rate, min_counts = mi_counts, min_cells = min_cells, min_gene_variability_pctl = min_gene_variability_pctl, n_prin_comps = n_prin_omps) 3: doScrubletDetect(DS_MERFISH, feat_type = NULL, spat_unit = "cell", expression_values = "raw", expected_doblet_rate = 0.06, min_counts = 1, min_cells = 1, min_gene_variability_pctl = 85, n_prin_comps = 100, retun_gobject = TRUE)