Missing platform information

Oct 13, 2025 by sorusgentrification.com 61 views

Resolving the "Not yet defined for the current platform" Error in SPATA2

The SPATA2 package is a powerful tool for single-cell analysis, particularly useful for downstream analysis of data from platforms like Merfish and Visium. However, when working with data from other sources, users may encounter the "Not yet defined for the current platform" error. In this article, we will explore the possible causes of this error and provide suggestions for resolving it.

The error message "Not yet defined for the current platform" is typically encountered when the simulate_complete_coords_sa() function is called. This function is responsible for simulating complete coordinates for a given object, but it requires specific information about the platform being used. If this information is not available, the function will throw an error.

There are several possible causes of the "Not yet defined for the current platform" error:

Missing platform information: The simulate_complete_coords_sa() function requires information about the platform being used, such as the Merfish or Visium platform. If this information is not available, the function will throw an error.
Incorrect object type: The simulate_complete_coords_sa() function is designed to work with specific types of objects, such as those created by the Seurat package. If the object being passed to the function is not of the correct type, the function will throw an error.
Incorrect distance or unit: The simulate_complete_coords_sa() function requires specific information about the distance and unit being used. If this information is not available or is incorrect, the function will throw an error.

To resolve the "Not yet defined for the current platform" error, you can try the following:

Check the platform information: Make sure that you have provided the correct platform information to the simulate_complete_coords_sa() function. If you are using data from a platform other than Merfish or Visium, you may need to modify the function to accommodate this.
Check the object type: Ensure that the object being passed to the simulate_complete_coords_sa() function is of the correct type. If the object is not of the correct type, you may need to modify the function to accommodate this.
Check the distance and unit: Make sure that you have provided the correct distance and unit information to the simulate_complete_coords_sa() function. If this information is not available or is incorrect, you may need to modify the function to accommodate this.

If you are unable to resolve the error by checking the platform information, object type, or distance and unit, you may need to modify the simulate_complete_coords_sa() function to accommodate your specific use case. This may involve adding additional arguments to the function or modifying the function to work with different types of objects.

Here is an example of how you might modify the simulate_complete_coords_sa() function to accommodate data from a platform other than Merfish or Visium:

simulate_complete_coords_sa <- function(object, id, distance, unit, platform = "Merfish") {
  # Check the platform information
  if (platform != "Merfish" && platform != "Visium") {
    stop("Not yet defined for the current platform")
  }
  
  # Simulate complete coordinates
  # ...
}

In this example, we have added a new argument platform to the simulate_complete_coords_sa() function. We then check the value of this argument to determine which platform is being used. If the platform is not Merfish or Visium, we throw an error.

The "Not yet defined for the current platform" error is a common issue encountered when working with the SPATA2 package. By understanding the possible causes of this error and modifying the simulate_complete_coords_sa() function to accommodate your specific use case, you can resolve this error and perform downstream analysis on your data.

For more information on the SPATA2 package and how to use it for downstream analysis, please refer to the following resources:

By following these resources and modifying the simulate_complete_coords_sa() function to accommodate your specific use case, you can successfully perform downstream analysis on your data using the SPATA2 package.
SPATA2 Q&A: Resolving the "Not yet defined for the current platform" Error

The SPATA2 package is a powerful tool for single-cell analysis, particularly useful for downstream analysis of data from platforms like Merfish and Visium. However, when working with data from other sources, users may encounter the "Not yet defined for the current platform" error. In this article, we will answer some frequently asked questions about resolving this error.

A: The "Not yet defined for the current platform" error is a common issue encountered when working with the SPATA2 package. It occurs when the simulate_complete_coords_sa() function is called, but the platform information is not available or is incorrect.

A: There are several possible causes of the "Not yet defined for the current platform" error:

Missing platform information: The simulate_complete_coords_sa() function requires information about the platform being used, such as the Merfish or Visium platform. If this information is not available, the function will throw an error.
Incorrect object type: The simulate_complete_coords_sa() function is designed to work with specific types of objects, such as those created by the Seurat package. If the object being passed to the function is not of the correct type, the function will throw an error.
Incorrect distance or unit: The simulate_complete_coords_sa() function requires specific information about the distance and unit being used. If this information is not available or is incorrect, the function will throw an error.

A: To resolve the "Not yet defined for the current platform" error, you can try the following:

Check the platform information: Make sure that you have provided the correct platform information to the simulate_complete_coords_sa() function. If you are using data from a platform other than Merfish or Visium, you may need to modify the function to accommodate this.
Check the object type: Ensure that the object being passed to the simulate_complete_coords_sa() function is of the correct type. If the object is not of the correct type, you may need to modify the function to accommodate this.
Check the distance and unit: Make sure that you have provided the correct distance and unit information to the simulate_complete_coords_sa() function. If this information is not available or is incorrect, you may need to modify the function to accommodate this.

A: To modify the simulate_complete_coords_sa() function to accommodate your specific use case, you can add additional arguments to the function or modify the function to work with different types of objects. For example, you can add a new argument platform to the function and check the value of this argument to determine which platform is being used.

A: There are several additional resources that you can use to learn more about the SPATA2 package and how to use it for downstream analysis:

Make sure to check the platform information, object type, and distance and unit information before calling the simulate_complete_coords_sa() function.
Modify the simulate_complete_coords_sa() function to accommodate your specific use case by adding additional arguments or modifying the function to work with different types of objects.
Use the additional resources provided to learn more about the SPATA2 package and how to use it for downstream analysis.