how to do noob+funnorm+bmiq normalization together in minfi or RnBeads?

Question

[rahel14350]

Dear all and Dear fortin946, I have data from cancer and healthy sample. I want to try to do noob+funnorm+bmiq for my data normalization. In minfi, I am only able to do preprocessFunnorm on my data. Do you have any idea, how I can add bmiq normalization? Is it possible in minfi or I should do it in RnBeads? Based on this paper: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2819-7#Sec2

Many thanks in advance, Rahel

[andrew.j.skelton73]

I wouldn't normally suggest this, but I think you'd have a better shot on Bioconductor support, as Kasper Hansen is on that mailing list when Minfi is tagged. No doubt Kasper would be able to give you a solid answer. Try to link to the post for future users.

Edit: I see you've already done that

[igor]

Can you clarify the problem? Why can you only use preprocessFunnorm? What is wrong with preprocessNoob?

[rahel14350]

I wanted to do different comparison on my data to check them (like the paper I addressed), I have high heterogeneity between my samples.