Skip to main content
Topic: Peak alignment with large dataset (over 2500 samples and growing) (Read 1500 times) previous topic - next topic

Re: Peak alignment with large dataset (over 2500 samples and growing)

Reply #30
Hello folks,

Some updates and a few more questions.

I have been using the 'IPO' package to determine my XCMS parameters. The resulting peak table contains over 50,000 features. I'm ok with this for now. Has anyone else used IPO? Thoughts?

I successfully ran CAMERA (thanks CoreyG for the suggestions) with the goal of finding redundant features (eg. adducts/isotopes). It identified~7,000 pc groups in the ~50,000 features. Now, if I am understanding correctly, I need to select one feature from each pc group to serve as the "representative" for that compound. Any recommendations on how to make this selection?

Many thanks!