Error EPICv2 ChAMP
2
@63a0c943
Last seen 9 days 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
• 205 views
@yuan-tian-13904
Last seen 8 days 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
@james-w-macdonald-5106
Last seen 1 hour ago
United States
It is not clear that you can use ChAMP for the EPICv2 arrays. You might consider instead using minfi directly.
before adding your answer.
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Or by using
devtoolslibrary function :(thank you for this great tool !)
You don't need to do either of the above suggestions.
will install without having to bother with how exactly it is being installed.