"Seems your IDAT file not from one Array"
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david.ch • 0
Last seen 4.2 years ago


I am analysis EPIC array. ChAMP.load gives me the following error message:

!!! Important !!! 
  Seems your IDAT file not from one Array, because they have different numbers of probe.
  ChAMP can not deal with mix Array, please reorganize your data.


I have only one array type, EPIC..


Any ideas or help is appreciated.

EPIC methylation ChAMP • 1.0k views
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Yuan Tian ▴ 250
Last seen 11 months ago
United Kingdom

Hello David:

Even EPIC array have different versions. For example, on Illumina website, you could find various versions of EPIC manifests. Version 2 have different number of CpG covered with version 4 if I remember correctly.

Different versions of EPIC data would have slightly differences on CpG covered, but should now be much. Thus, a proper way to address this problem is extracting common CpGs in these samples.

However, I still suggest you check your samples IDAT data, you just need to us bath command to list their file size, then you should be able to find differences between samples. Then, after loading, I suggest you load this information into pd as a covariate, then see if it has system bias to final data set.


Yuan Tian

Entering edit mode
Last seen 9 months ago
United Kingdom

If using the 'minfi' method, you can use 'force = TRUE'. As Yuan said above, the current Illumina EPIC manifest is in its 4th version of revisions. With each version they drop some poor performing probes and I think B3 had some naming issues. The minfi function used by ChAMP will force the import of IDATs to combine arrays with different numbers of probes (within reason). 

If you do have 450K and EPIC data combined, you'll still get issues. Easiest way to check would be to look at the IDAT file sizes. A normal 450K IDAT is around 7MB, while an EPIC IDAT is around 11MB in size.

Entering edit mode

Hello Yura,

No, I don't have 450K and EPIC combined. Its only EPIC array.

I changed the method to "minfi" and "force=true", as you suggested and it worked. Thanks.





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