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Question: Pre-processing and probe removal in lumi
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gravatar for Matthias Zilbauer
4.8 years ago by
Matthias Zilbauer30 wrote:
Dear all, I am working on some Illumina K450 methylation array data using mainly the lumi package. As part of the pre-processing I would like to remove all probes within known SNPs and probes with ambiguous alignments. Unfortunately there is no pre-set function provided and I can't get it to work myself. Any suggestions would be much appreciated. Many thanks in advance Matt [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.8 years ago by Lavinia Gordon480 • written 4.8 years ago by Matthias Zilbauer30
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gravatar for Lavinia Gordon
4.8 years ago by
Lavinia Gordon480 wrote:
Hi Matt, Not sure about lumi, only use it for HM27 data (for which it is great), not sure how well it works with HM450. Take a look at the package minfi and also the annotation packages *450*, e.g. IlluminaHumanMethylation450k.db, Tim Triche Jr. has put some nice well-documented code in these vignettes which may prove helpful. Regards, Lavinia Gordon Senior Research Officer Quantitative Sciences Core, Bioinformatics Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com
ADD COMMENTlink written 4.8 years ago by Lavinia Gordon480
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