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xzhoulab / SPARK-Analysis

spatially resolved data analysis
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Question about simulation data #4

Open yukilh opened 2 years ago

yukilh commented 2 years ago

Hi, thank you for such an excellent SPARK software！

I'm currently working on spatial transcriptomic data, and want to use SPARK for some analysis. I checked the analysis steps you gave in github, and am very interested in the analysis of simulated data.

But when I looked through the "simulation/simulation_mouse_ob.R" file in it, I couldn't find the "Rep11_MOB_spark.rds" file used in the Data Generation and Noise Change steps.

Perhaps, would it be convenient to tell me how to get this rds file, or how this file is generated? It would be nice if you could provide a bit more information on the simulation steps.

jakezhusph commented 2 years ago

Hi, thank you for such an excellent SPARK software！

I'm currently working on spatial transcriptomic data, and want to use SPARK for some analysis. I checked the analysis steps you gave in github, and am very interested in the analysis of simulated data.

But when I looked through the "simulation/simulation_mouse_ob.R" file in it, I couldn't find the "Rep11_MOB_spark.rds" file used in the Data Generation and Noise Change steps.

Perhaps, would it be convenient to tell me how to get this rds file, or how this file is generated? It would be nice if you could provide a bit more information on the simulation steps.

Hi, thanks for your interest in SPARK. You can get the "Rep11_MOB_spark.rds" by running the SPARK on the MOB data and save it as the name shown here. We didn't provide this, as the file size is too big for a regular github account. Moreover, you can find the simulation details in the manuscript and the supplementary file. Let me know if you have any further questions. Best :)

yukilh commented 2 years ago

Hi, thank you for such an excellent SPARK software！ I'm currently working on spatial transcriptomic data, and want to use SPARK for some analysis. I checked the analysis steps you gave in github, and am very interested in the analysis of simulated data. But when I looked through the "simulation/simulation_mouse_ob.R" file in it, I couldn't find the "Rep11_MOB_spark.rds" file used in the Data Generation and Noise Change steps. Perhaps, would it be convenient to tell me how to get this rds file, or how this file is generated? It would be nice if you could provide a bit more information on the simulation steps.

Hi, thanks for your interest in SPARK. You can get the "Rep11_MOB_spark.rds" by running the SPARK on the MOB data and save it as the name shown here. We didn't provide this, as the file size is too big for a regular github account. Moreover, you can find the simulation details in the manuscript and the supplementary file. Let me know if you have any further questions. Best :)

Thank you for your reply! I have successfully generated this rds file now :)