search

aerickso / SpatialInferCNV

Clone Calling from Visium Spatial Transcriptomics of Cancer samples
55 stars 13 forks source link

Questions about my results #7

Open yunbokai opened 1 year ago

yunbokai commented 1 year ago

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? 图片 Best wishes.

aerickso commented 1 year ago

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 commented 1 year ago

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.