ICA – Reconstruction Errors

ICA – Reconstruction Errors

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Hello people! I am completely new to the topic of ML and Omics and at all in the bioinformatics field. To gather some knowledge I started to work through a book I found on the internet and there is the following task:

“Produce a 10-component ICA from the expression data set. Remove each component and measure the reconstruction error without that component. Rank the components by decreasing reconstruction-error. [Difficulty: Advanced]”

So I kind of understood what the reconstruction error is (so the differences of the points that are “reconstructed” from my component analyses to the acutall points.). But I am kind of struggeling to think through that thing. Would there be someone that could help me with that and explain on the way for a total beginner 🙂 Would be awesome!

Some background for the task:

  • expression data is from leukemia patients (ALL, CML, AML, CLL and no-leukemia)
  • rows are the genes (ENSG ….)
  • colums are the cells (ALL_GSM330151.CEL)
  • dim(df) = 60 1000

And here would be the book with the exercise:

https://compgenomr.github.io/book/exercises-2.html

(second question from the bottom of the page)


ML


Newbie


ICA


Omics

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