Error while running find_neighbors2( )

[anashank]

Hello,

I am trying to run the SC-MEB pipeline on my dataset. I ran the preprocess step, but I am getting the following error while trying to find neighbors:

Adj_sp <- find_neighbors2(sample.sce,platform="Visium") Error: subscript contains invalid names

I am not sure why this is happening. Any suggestions on how I can debug this? Thanks!

[Shufeyangyi2015310117]

you can try the find_neighbors() from the BayesSpace, which is attached. It that cannot work, maybe your sce object have some problems. Yang YiBest regards

----- 原始邮件 ----- 发件人：Anand Shankar @.> 收件人："Shufeyangyi2015310117/SC.MEB" @.> 抄送人：Subscribed @.***> 主题：[Shufeyangyi2015310117/SC.MEB] Error while running find_neighbors2( ) (#1) 日期：2021年10月08日 07点11分

Hello, I am trying to run the SC-MEB pipeline on my dataset. I ran the preprocess step, but I am getting the following error while trying to find neighbors: Adj_sp <- find_neighbors2(sample.sce,platform="Visium") Error: subscript contains invalid names I am not sure why this is happening. Any suggestions on how I can debug this? Thanks!

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[anashank]

Thanks, is there any specific format that is required for the input sce object?

[anashank]

Also, could you please tell me how I should use the BayesSpace .find_neighbors( ) function, I was having difficulty running it, the dot in front of the function name seems to be a bit confusing, I have never encountered an R function like this before

[Shufeyangyi2015310117]

you can refer to the simulation example in the vignette of SC.MEB to construct a sce like that, it only require the count matrix and spatial information. Thank youYangYiBest regards ----- 原始邮件 ----- 发件人：Anand Shankar @.> 收件人："Shufeyangyi2015310117/SC.MEB" @.> 抄送人：Shufeyangyi2015310117 @.>, Comment @.> 主题：Re: [Shufeyangyi2015310117/SC.MEB] Error while running find_neighbors2( ) (#1) 日期：2021年10月08日 12点53分

Thanks, is there any specific format that is required for the input sce object?

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[Shufeyangyi2015310117]

I have included the find_neighbors() function in the attachment. you can directly use it. you can use it in the same way of find_neighbors2(). you don't need download it from BayesSpace. Thank youYang YiBest regards

----- 原始邮件 ----- 发件人：Anand Shankar @.> 收件人："Shufeyangyi2015310117/SC.MEB" @.> 抄送人：Shufeyangyi2015310117 @.>, Comment @.> 主题：Re: [Shufeyangyi2015310117/SC.MEB] Error while running find_neighbors2( ) (#1) 日期：2021年10月08日 12点55分

Also, could you please tell me how I should use the BayesSpace .find_neighbors( ) function, I was having difficulty running it, the dot in front of the function name seems to be a bit confusing, I have never encountered an R function like this before

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[Shufeyangyi2015310117]

you tell me your email, I can send it to you. Thank youYang YiBest regards----- 原始邮件 ----- 发件人：Anand Shankar @.> 收件人："Shufeyangyi2015310117/SC.MEB" @.> 抄送人：Shufeyangyi2015310117 @.>, Comment @.> 主题：Re: [Shufeyangyi2015310117/SC.MEB] Error while running find_neighbors2( ) (#1) 日期：2021年10月08日 12点55分

Also, could you please tell me how I should use the BayesSpace .find_neighbors( ) function, I was having difficulty running it, the dot in front of the function name seems to be a bit confusing, I have never encountered an R function like this before

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[anashank]

Thanks a lot, I was able to get it to work!