8000 Error Error in norm_cords$x - min(norm_cords$x) : non-numeric argument to binary operator · Issue #70 · YMa-lab/CARD · GitHub
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Error Error in norm_cords$x - min(norm_cords$x) : non-numeric argument to binary operator #70

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krigia opened this issue Mar 16, 2024 · 1 comment
Open

Error Error in norm_cords$x - min(norm_cords$x) : non-numeric argument to binary operator #70

krigia opened this issue Mar 16, 2024 · 1 comment

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@krigia
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krigia commented Mar 16, 2024

Hello @YingMa0107 @YMalab > # Make CARD object

CARD_obj = createCARDObject(

  • sc_count = sc_count,
  • sc_meta = sc_meta,
  • spatial_count = spatial_count,
  • spatial_location = spatial_location,
  • ct.varname = "cellType",
  • ct.select = unique(sc_meta$cellType),
  • sample.varname = "sampleInfo",
  • minCountGene = 100,
  • minCountSpot = 5)

QC on scRNASeq dataset! ...

QC on spatially-resolved dataset! ...

Run CARD deconvolution

CARD_obj = CARD_deconvolution(CARD_object = CARD_obj)

create reference matrix from scRNASeq...

Select Informative Genes! ...

Error in norm_cords$x - min(norm_cords$x) :
non-numeric argument to binary operator
In addition: Warning messages:
1: In asMethod(object) :
sparse->dense coercion: allocating vector of size 5.6 GiB
2: In asMethod(object) :
sparse->dense coercion: allocating vector of size 2.9 GiB
3: In asMethod(object) :
sparse->dense coercion: allocating vector of size 2.1 GiB
4: In asMethod(object) :
sparse->dense coercion: allocating vector of size 2.1 GiB

I was wondering if this could be related to count data or spatial coordinates. I used spot barcode IDs instead of number x,y coordinates. e. g.
x() TACGATCCAAGCCACT-1_1
y()TACGATCCAAGCCACT-1_1
Also, sc and spatial counts are row filtered data.

Please advise. Thank you.
@YMalab
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YMalab commented Apr 1, 2024 •
edited
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Hi @krigia,

What does your spatial_location matrix look like? This matrix should contain the spatial coordinates. Please follow our tutorial to check if you input data match exactly with the tutorial example data format. Thanks.

Best,
Ying

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@krigia @YMalab
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