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?