Error in h(simpleError(msg, call)) :

[Qiannnzzz]

hi beibei, There is an error, and I don't know how to fix it. the platform of data is Stereo-seq.

best,
Qian

[beibeiru]

Hi, Qian,

Please upload your SpaCET_obj to the following folder and also show your code. I will fix it soon.

Best,
Beibei

[Qiannnzzz]

Hi, Beibei, I upload the SpaCET_obj. Best, Qian

…

On Mar 21, 2024, at 10:21 AM, Beibei Ru ***@***.***> wrote: Hi, Qian, Please upload your SpaCET_obj to the following folder and also show your code. I will fix it soon. https://connecthkuhk-my.sharepoint.com/:f:/g/personal/bbru_connect_hku_hk/EvSjqxDECX1Fln-eNp6viLkBzcqeWsu11gRWz1SY32Ux8g?e=XEOxsK Best, Beibei — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BEVKDCPSJRZPTAHQQQ2FAR3YZI72LAVCNFSM6AAAAABFAOZ6CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJRGA3DSMZVG4>. You are receiving this because you authored the thread.

[Qiannnzzz]

Hi Beibei, I noticed in the same analysis environment, that some samples can run normally, some not. The sample size of the two types is similar, even the data format is the same. So I want to know why. It confuses me a lot. From the error information, I think the reason is the Matrix library, I updated it from 1.5 to 1.6, and SpaCET still doesn’t work. Best, Qian

…

On Mar 21, 2024, at 10:21 AM, Beibei Ru ***@***.***> wrote: Hi, Qian, Please upload your SpaCET_obj to the following folder and also show your code. I will fix it soon. https://connecthkuhk-my.sharepoint.com/:f:/g/personal/bbru_connect_hku_hk/EvSjqxDECX1Fln-eNp6viLkBzcqeWsu11gRWz1SY32Ux8g?e=XEOxsK Best, Beibei — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BEVKDCPSJRZPTAHQQQ2FAR3YZI72LAVCNFSM6AAAAABFAOZ6CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJRGA3DSMZVG4>. You are receiving this because you authored the thread.

[beibeiru]

Hi, Qian,

The error you've got was caused by some extremely low-quality spots (i.e., bins) in your current data although you have done quality control. You can select any one of the following options to address it.

1. do SpaCET.quality.control again and set min.genes to a higher value (default is 1).
2. reinstall SpaCET and still use your current code because I have fixed this bug in the new version.

I recommend the second option. Please let me know whether it works for you.

Best,
Beibei

[Qiannnzzz]

Hi, Beibei, Thank you very much for fixing this bug, I’ll try the second option. Best, Qian

…

On Mar 22, 2024, at 3:06 AM, Beibei Ru ***@***.***> wrote: Hi, Qian, The error you've got was caused by some extremely low-quality spots (i.e., bins) in your current data although you have done quality control. You can select any one of the following options to address it. do SpaCET.quality.control again and set min.genes to a higher value (default is 1). reinstall SpaCET and still use your current code because I have fixed this bug in the new version. I recommend the second option. Please let me know whether it works for you. Best, Beibei — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BEVKDCKOWCT6NX2K52LIL6LYZMVTRAVCNFSM6AAAAABFAOZ6CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJTGM3DKMBSGE>. You are receiving this because you authored the thread.