how to do noob+funnorm+bmiq normalization together in minfi or RnBeads?
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rahel14350 ▴ 10
@rahel14350-8472
Last seen 3.6 years ago
United States

Dear Kasper Daniel Hansen,

Can you please help me with this question on Biostar (https://www.biostars.org/p/245859/).

I want to do noob+funnorm+bmiq normalization on cancer samples using minfi. Is this possible? 

Many thanks in advance,

Rahel

minfi RnBeads noob preprocessFunnorm BMIQ • 1.5k views
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@kasper-daniel-hansen-2979
Last seen 8 days ago
United States
It is not clear that combining two preprocessing methods is better than using either one of them individually. It is probably possible to hack the functions to do what you want, but it is not trivial, and it is not clear it is even a good idea. Best, Kasper On Wed, Apr 5, 2017 at 11:35 AM, rahel14350 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User rahel14350 <https: support.bioconductor.org="" u="" 8472=""/> wrote Question: > how to do noob+funnorm+bmiq normalization together in minfi or RnBeads? > <https: support.bioconductor.org="" p="" 94563=""/>: > > Dear Kasper Daniel Hansen <https: support.bioconductor.org="" u="" 2979=""/>, > > Can you please help me with this question on Biostar ( > https://www.biostars.org/p/245859/). > > I want to do noob+funnorm+bmiq normalization on cancer samples using > minfi. Is this possible? > > Many thanks in advance, > > Rahel > > ------------------------------ > > Post tags: minfi, RnBeads, noob, preprocessFunnorm, BMIQ > > You may reply via email or visit how to do noob+funnorm+bmiq normalization together in minfi or RnBeads? >
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Dear Kasper Daniel Hansen,

Many thanks for prompt reply. I got the idea from this paper, as they showed it is working better on cancer data. It is also because I have a high heterogeneity and variation between my samples and I wanted to compare different normalization possibilities. 

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2819-7#Sec2

Kind Regards, Rahel

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