Error code using ChAMP/Bioconductor, unable to load data from EPIC methylation array

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csappleby-mallinder1 • 0

@csappleby-mallinder1-14812

Last seen 6.2 years ago

Hello,

I am trying to use ChAMP to analyse the data from 2 microarray chips (Illumina Infinium EPIC arrays), however, I get this error message:

Loading data from ../chips
[read.metharray.sheet] Found the following CSV files:
[1] "../chips/Sample_Sheet.csv"
Error: !anyDuplicated(basenames) is not TRUE

This is the code I used to load my data into ChAMP:

> myLoad<-champ.load("../chips",method="minfi",arraytype="EPIC")

I am very new to using Bioconductor/ChAMP, so am unsure what to do to rectify this in order to load my data..

Any help would be greatly appreciated!

bioconductor methylation epic microarray champ • 2.0k views

ADD COMMENT • link 6.3 years ago csappleby-mallinder1 • 0

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Hello:

I suspect something wrong with your Sample_Sheet.csv file. Could you sent it to champ450K@gmail.com for me to check? I suspect your basename is duplicated, which means champ can not extract name for your IDAT data.

Best

Yuan Tian

ADD REPLY • link 6.3 years ago Yuan Tian ▴ 280

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Hi Yuan Tian,

Many thanks for your assistance. I have now been able to load the data, but am now having this error message:

Error in champ.import(directory, arraytype = arraytype) :
Meth Matrix and UnMeth Matrix seems not paried correctly

Best wishes

Charlie

ADD REPLY • link 6.2 years ago csappleby-mallinder1 • 0

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