Error EPICv2 ChAMP
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@63a0c943
Last seen 4 weeks ago
Italy

Hi everyone, can anyone help me solve this problem with the ChAMP library (2.29.1), it tells me Anno not found in section 3 of Use Annotation Start

``` myImport<-champ.load(directory=getwd(),arraytype="EPICv2")

[ Section 3: Use Annotation Start ] ....

Error in rownames(Anno$ControlProbe) : object 'Anno' not found In addition: Warning messages: 1: In readLines(csvfile) : incomplete final line found on '/Users/aur/Desktop/Array/208160850024/Sample_Sheet_28_03_24.csv' 2: In data("AnnoEPICv2") : data set 'AnnoEPICv2' not found

ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP • 312 views
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Yuan Tian ▴ 290
@yuan-tian-13904
Last seen 4 weeks ago
United Kingdom

You also need to install the matched ChAMPdata to use EPICv2. As the instruction here.

Run below code to install the ChAMPdata contains EPICv2 annotation.

git clone https://github.com/YuanTian1991/ChAMPdata.git
R CMD INSTALL ChAMPdata
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Or by using devtools library function :

install_github("YuanTian1991/ChAMPdata")

(thank you for this great tool !)

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You don't need to do either of the above suggestions.

library(BiocManager)
install("YuanTian1991/ChAMPdata")

will install without having to bother with how exactly it is being installed.

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@james-w-macdonald-5106
Last seen 17 minutes ago
United States

It is not clear that you can use ChAMP for the EPICv2 arrays. You might consider instead using minfi directly.

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