Questions about my results

[yunbokai]

Hi,
Thanks for your package.
I used spatialCNV in my 10x Visium data(HNSCC) with the code provided in tutorial. I selected all spots in order to depict my clone condition. However, the result is strange.
I have no idea that what happened. Could you please give me some advice?

Best wishes.

[aerickso]

Hi!

Thank your for your interest.

Are you using a reference set? Can you copy-paste your code chunk for setting up the unsupervised analysis?

Example from figure 2: https://github.com/aerickso/SpatialInferCNV/blob/main/FigureScripts/Figure%202/Step1/Figure2_AllCancer_siCNV_step1_unsupervised.md#unsupervised-run---typically-ran-on-cluster

[yunbokai]

Hello @aerickso , I'm here to discuss my data usage with you. As I previously mentioned in an issue, I encountered many problems when using the package, including abnormal results and errors. Later, I accidentally discovered that setting the function run() as follows: tumor_subcluster_partition_method = "random_trees", all the results were smooth and I obtained some valuable information. I asked the author of inferCNV, but he couldn't fully explain the situation and mentioned that some people may have had similar problems, but not sure if it's related to spatial data. I would like to hear your thoughts on this. Thans for your help.

[rhlgyb]

Hi,
Have you received any additional help after this post or have come across new realizations?
I am seeing the same results with my data am not sure how to interpret it.

Thanks.