Calculatin ANOVA between two files with 50x1000 matrix

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Hello, I have 4 files with a 50x1000 matrices. Where n=50 is the number of repetition of a task and 1000 is the number of frames. Now I want to compare this files with an ANOVA. How can I do that? I only found the solution from Matlabe, which compares the coloums in one file.
Thanks for your help! Oliver

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