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YuanTian1991 / ChAMP

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Bug: In champ.import (ChAMP "2.30.0") #43

Open MitaliKatoch opened 9 months ago

MitaliKatoch commented 9 months ago

Hey, I am working on EPICv2 data. ChAMP ("2.30.0"), ChAMPdata ("2.34.0"). Error:

Meth Matrix and UnMeth Matrix seems not paried correctly.

With: champ.load(directory = dir_idats, arraytype = 'EPIC') I am getting following error

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, arraytype = arraytype) : Meth Matrix and UnMeth Matrix seems not paried correctly.

When arraytype= is either EPICv1 or EPICv2 Error:

Reading EPICv2 Annotation >>

Fetching NEGATIVE ControlProbe. Totally, there are 613 control probes in Annotation. Your data set contains 281 control probes.

Generating Meth and UnMeth Matrix Extracting Meth Matrix... Totally there are 485512 Meth probes in EPICv2 Annotation. Your data set contains 485512 Meth probes. Extracting UnMeth Matrix... Totally there are 485512 UnMeth probes in EPICv2 Annotation. Your data set contains 485512 UnMeth probes. Error in champ.import(directory, arraytype = arraytype) : Meth Matrix and UnMeth Matrix seems not paried correctly.

Why does the UnMeth probe number vary in EPICv2 and EPIC? Even though:

Since version 2.29.1, ChAMP set default EPIC arraytype as EPIC version 2. ", You can set 'EPIC' or 'EPICv2' to use version 2 EPIC annotation. If you want to use the old version (v1), please specify arraytype parameter as EPICv1. For 450K array, still use 450K")

Can someone help me with this? Is it a bug? Is the not paried correctly error a result of this bug?

MitaliKatoch commented 9 months ago

I figured out now that the latest release does not contain AnnoEPICv2 . After downgraded to ChAMP"2.29.1" and ChAMPdata"2.31.1", it's working!

Guoge1212 commented 7 months ago

I am currently using the latest version of the "ChAMP" package, version 2.32, but I am still encountering the error mentioned above. I would like to download version 2.29.1 of "ChAMP". However, I am unable to find this specific version either on the GitHub main page or on the Bioconductor historical versions page. Could you please explain how you managed to download version 2.29.1 of "ChAMP"?