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JEFworks-Lab / STdeconvolve

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
http://jef.works/STdeconvolve/
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Visium 'se' object creation error #50

Open Umaarasu opened 9 months ago

Umaarasu commented 9 months ago

Hi,

I have tried to run my data using your visium tutorial. I keep getting this error in the initial step. This happens with both your example data and my data. Could you please tell me how to sort this out.

f <- "visiumTutorial/" if(!file.exists(f)){ dir.create(f) }

se <- SpatialExperiment::read10xVisium(samples = f, type = "sparse", data = "filtered") Error in names(xyz) <- names(sfs) <- sids : 'names' attribute [1] must be the same length as the vector [0]

bmill3r commented 9 months ago

Hi @Umaarasu,

I am not sure exactly what is going on but seems to be an error within SpatialExperiment. Did you download and unzip the files in the step before? Sorry I can't be more helpful.

Brendan

changuniuni commented 9 months ago

Even though I followed all the steps @bmill3r mentioned, I'm having the same problem. @Umaarasu If you solved it, could you let me know how to solve it?

Umaarasu commented 9 months ago

@bmill3r @changuniuni ..looks like there was a issue with SpatialExperiment command. I implemented the STdeconv as mentioend below for my data. The whole pipeline for visium STdeonvolv ran without any error.

sample_dir <- "/Visium/outs/" se <- read10xVisium(samples = sample_dir, type = "sparse", data = "filtered", images = "lowres", load = TRUE)