Error in wilcox.test

[thineskrishna]

Hi Thank you for creating this tool.

I come across the following error and any advice is appreciated

SpaCET_obj <- SpaCET.deconvolution(SpaCET_obj, cancerType="PRAD", coreNo=8)
[1] "Stage 1. Infer malignant cell fraction."
[1] "Stage 1 - Step 1. Clustering."
[1] "Stage 1 - Step 2. Find tumor clusters."
Error in wilcox.test.default(cor_sig_clustering[, 1], mu = 0, alternative = "greater") :
not enough (non-missing) 'x' observations
In addition: Warning message:
In sqrt(n - 2) : NaNs produced

I have included link to my SpaCET_obj for your reference
https://drive.google.com/file/d/1kMSlQC8FZ1vcd1G2AJkNlUa91hwtxdCp/view?usp=drive_link

Many thanks

[beibeiru]

Hi, @thineskrishna

Thank you for your interest in SpaCET.

The error is caused by the existence of a few low-quality spots (no gene detected in these spots) in your input ST data.
You can use SpaCET.quality.control to filter spots first, which is shown below.

> load("SpaCET_obj.RData")
> SpaCET_obj <- SpaCET.quality.control(SpaCET_obj)
[1] "19 spots are removed."
[1] "2756 spots are kept."
> SpaCET_obj <- SpaCET.deconvolution(SpaCET_obj, cancerType="PRAD", coreNo=8)
[1] "Stage 1. Infer malignant cell fraction."
[1] "Stage 1 - Step 1. Clustering."
[1] "Stage 1 - Step 2. Find tumor clusters."
[1] "                  > Use CNA signature: PRAD"
[1] "Stage 1 - Step 3. Infer malignant cells."
[1] "Stage 2. Hierarchically deconvolve non-malignant cell fraction."
[1] "Stage 2 - Level 1. Estimate the major lineage."
[1] "Stage 2 - Level 2. Estimate the sub lineage."

Please let me know if you have any further questions.

Best,
Beibei