Error EPICv2 ChAMP
2
@63a0c943
Last seen 8 months 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
• 874 views
@yuan-tian-13904
Last seen 8 months 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 14 hours 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.