Question: Error code using ChAMP/Bioconductor, unable to load data from EPIC methylation array
gravatar for csappleby-mallinder1
19 months ago by
csappleby-mallinder10 wrote:



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!

ADD COMMENTlink written 19 months ago by csappleby-mallinder10


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


Yuan Tian

ADD REPLYlink written 19 months ago by Yuan Tian110

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


ADD REPLYlink written 19 months ago by csappleby-mallinder10
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