Question

Error using champ.import

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medha.suman • 0

@5f773e94

Last seen 17 months ago

Sweden

Hi,

I am working with EPIC v2 methylation data and trying to read the data using champ.import function. But i am getting the below error message.

data = champ.import(directory = "~/Documents/EPIC_may/IDATs/", arraytype = "EPICv2")

[===========================]
[<<<< ChAMP.IMPORT START >>>>>]
-----------------------------

[ Section 1: Read PD Files Start ]
  CSV Directory: /Users/medha/Documents/EPIC_may/IDATs//pd_MS.csv
  Find CSV Success
  Reading CSV File
  Replace Sentrix_Position into Array
  Replace Sentrix_ID into Slide
[ Section 1: Read PD file Done ]


[ Section 2: Read IDAT files Start ]
  Loading:/Users/medha/Documents/EPIC_may/IDATs//207218120055_R01C01_Grn.idat ---- (1/96)
  Loading:/Users/medha/Documents/EPIC_may/IDATs//207218120055_R02C01_Grn.idat ---- (2/96)
.
.
.

  Loading:/Users/medha/Documents/EPIC_may/IDATs//207215830010_R08C01_Red.idat ---- (96/96)

  Extract Mean value for Green and Red Channel Success
    Your Red Green Channel contains 1105209 probes.
[ Section 2: Read IDAT Files Done ]


[ Section 3: Use Annotation Start ]

  Reading EPIC Annotation >>

  Fetching NEGATIVE ControlProbe.
    Totally, there are 411 control probes in Annotation.
    Your data set contains 411 control probes.

  Generating Meth and UnMeth Matrix
    Extracting Meth Matrix...
      Totally there are 865918 Meth probes in EPIC Annotation.
      Your data set contains 865918 Meth probes.
    Extracting UnMeth Matrix...
      Totally there are 865918 UnMeth probes in EPIC Annotation.
      Your data set contains 865918 UnMeth probes.
Error in champ.import(directory = "~/Documents/EPIC_may/IDATs/", arraytype = "EPICv2") : 
    Meth Matrix and UnMeth Matrix seems not paried correctly.


sessionInfo( )
R version 4.2.3 (2023-03-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.0.1

Any Idea/suggestions on how to solve this.

Thanks, Medha.

ChAMP EPICv2 • 3.0k views

ADD COMMENT • link updated 8 weeks ago by Ricky • 0 • written 17 months ago by medha.suman • 0

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Have you checked the answers here ? : Problem at champ.load

ADD REPLY • link 17 months ago Basti ▴ 780

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Hi, I have also the same problem. Any hints on how to resolve it? thanks

ADD REPLY • link 16 months ago Fulvio • 0

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Did you read the post that Basti linked to?

ADD REPLY • link 16 months ago James W. MacDonald 67k

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I have exactly the same problem and I never had this problem with Epic V1. The answer posted in the link is not the same problem as the one we are having. That problem is that there were different numbers of Unmeth and meth probes. This problem is that the numbers are the same but their annotation is different. This is likely down to EPIC v2 probe annotation and it may be that we can no longer use ChAMP pipeline on it without a fix

ADD REPLY • link 13 months ago wellitonboots • 0

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The ChAMP pipeline doesn't recognize the difference between the V1 and V2 arrays. This is also true for minfi, but it's simple to fix that situation. You will have to install the annotation packages that Zuguang Gu generated using

library(BiocManger)
install("jokergoo/IlluminaHumanMethylationEPICv2manifest")
install("jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38")

And then change the annotation of your RGset after you read in the data.

ADD REPLY • link 13 months ago James W. MacDonald 67k

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Thank you very much for this comment. The annotation packages that Zuguang Gu generated worked well for me in the minfi pipeline, but not in ChAMP. Have someone managed to run it in ChAMP?

ADD REPLY • link 10 months ago fernanda.hackenhaa • 0

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I'm having same issues too. Did anyone manage to resolve it?

ADD REPLY • link 8 months ago shilpa • 0

score 0 · Answer 1 · 2024-05-31

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549823162 • 0

@dd350a57

Last seen 6 months ago

Hong Kong

The new version 2.29.1 could support EPICv2. see https://github.com/YuanTian1991/ChAMP

ADD COMMENT • link 6 months ago 549823162 • 0

score 0 · Answer 2 · 2024-10-17

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Ricky • 0

@0f3288f8

Last seen 8 weeks ago

United States

I had similar issues. The workaround is to use ChAMP v2.29.1 and also use ChAMPdata 2.31.1.

Installation was done using the following on the command line:

git clone https://github.com/YuanTian1991/ChAMP.git

R CMD INSTALL ChAMP

git clone https://github.com/YuanTian1991/ChAMPdata.git

R CMD INSTALL ChAMPdata

ADD COMMENT • link 8 weeks ago Ricky • 0