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Minfi returning different beta values from GEO

I'm using the Minfi package to retrieve beta values from idat files from a study from GEO. The study on GEO had both beta values and the idat files. However the beta values I got from Minfi and the beta values on GEO are slightly different.

The study was published in 2015 and the Minfi package I'm using has been updated in 2017. Do you think that Minfi is making the beta values more accurate and I should just ignore the differences in beta values?

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written by ezrabekele17 • ezrabekele17

Hello ezrabekele17!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/97979/

This is typically not recommended as it runs the risk of annoying people in both communities.

The other site also got far more information on what's going wrong.

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written by WouterDeCoster WouterDeCoster

Hello ezrabekele17!

We believe that this post does not fit the main topic of this site.

Crossposted to two others sites, more information on other sites

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by WouterDeCoster WouterDeCoster

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