Comments (7)
Hi @shahrozeabbas , there has been an ongoing discussion regarding the issue (#9), and I've made some recent changes to mitigate. Can you try installing the latest SpotClean version?
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@zijianni Ahh okay thanks for pointing that out to me. I opted for the bioconda installation and it uses version 1.2, will give it a try and update!
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@zijianni Hi, I've tried this a couple of different ways and am still getting the same error. I tried with both Seurat 4.4 and Seurat 5. Any idea what might be happening? Looking forward to using this tool. Thanks for your help!
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@zijianni It looks like the Bioconductor version is 1.4 and the GitHub version is 1.5, both are producing the same error it seems.
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Were you able to check #9 to see anything helpful there? If you could share more info about your data (e.g. proportion of tissue and non-tissue spots in your slide) that would also be helpful.
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Yes I am currently checking with the sequencing team regarding the presence of non-tissue spots. It seems as though certain samples only detected spots with tissue. Which would explain why some are failing and others are not. Will update, thank you for your help so far!
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@zijianni Just to confirm that I am using the raw counts file from SpaceRanger
. My code below:
slide_object <- SpatialExperiment::read10xVisium(samples='data/Y1FA_out/outs', data='raw')
clean_object <- SpotClean::spotclean(slide_object)
object <- SpotClean::convertToSeurat(clean_object, image_dir='data/Y1FA_out/outs/spatial/')
It seems that some of the raw files don't include non-tissue specific spots because they were manually selected excluding those spots. We are rerunning SpaceRanger
which I hope will include all non-tissue specific spots in the raw counts file. I will rerun SpotClean
and let you know if everything is good. I suspect the error I am getting is due to an absence of non-tissue spots.
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Related Issues (20)
- install for R <= 4.1.3 HOT 3
- Adapt to Spaceranger 2.0 output HOT 1
- Error in optim(x_init, .fn_optim, .gr_optim, method = "L-BFGS-B", obs_exp = obs_exp, : non-finite value supplied by optim HOT 15
- SpatialExperiment::spatialData now deprecated HOT 1
- Questions about tissue regions HOT 2
- Questions about the output HOT 1
- How to modify strength of SpotClean? HOT 5
- Issue due to missing spot barcodes in raw matrix HOT 10
- could spotclean work under situation that all spot 's tissue==1? that my ST data 's tissue position csv 's tissue is all 1,no o,that no backgroud spot HOT 3
- The "max difference of decontaminated expressions" HOT 4
- How to run with large datasets in limited memory? HOT 2
- Error in createSlide(), 'barcodes in count matrix do not match barcodes in slide info' HOT 9
- The tissue photographs were presented in the wrong horizontal and vertical ratio HOT 2
- Error in convertToSeurat function, "Error in FUN(left, right) : non-numeric argument to binary operator" HOT 2
- Prepare for upcoming Seurat v5 release HOT 1
- SpotClean performance on 11x11mm slides and questions regarding to output HOT 1
- Ensembl IDs to Gene Names
- Error in keepHighGene(raw_ts_data, verbose = verbose) : no slot of name "meta.data" for this object of class "Assay" HOT 5
- Spotclean() stalls on testdata HOT 2
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