Hello everyone,

I am currently using the TCGAbiolinks package and attempting to apply the TCGAanalyze_SurvivalKM function for survival analysis. However, I've encountered several issues that I hope to get assistance with.

1) Error Related to Filter Method: When I run the function, I receive the error:

Error in UseMethod("filter") : 

no method for 'filter' applicable for an object of class "c('matrix', 'array', 'double', 'numeric')".

This error occurs when I try to filter data based on specific criteria.

2) Duplicate Names Issue: Additionally, when attempting to transform my dataGE data frame into a matrix, I get the following error: Can't transform a data frame with duplicate names.

I have checked my data and do not see any duplicates.

3) Unrecognized Objects: I also faced an error stating that the object ThreshTop is not found:

Error: object 'ThreshTop' not found.

4) Issues with Thresholds: When setting thresholds for my analysis, I am unsure whether I should simply input values like 0.67 and 0.33 for ThreshTop and ThreshDown.

5) Handling Missing Elements: Lastly, I receive an error related to the lastelementTOP object being undefined:

Error in .fun(piece, ...) : object 'lastelementTOP' not found

This happens when no values exceed the defined thresholds.

I have tried to work with the source code to debug these issues further but have not found a resolution.

I would greatly appreciate any guidance on how to resolve these problems. Thank you in advance for your help!