single excel file containing methylation beta values does not get loaded in ChAMP
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Last seen 17 days ago

Hello, I have an excel sheet with all the beta values and probe IDs. I also created a pd file in the same directory (containing sentrix id, sentrix position etc). However when I try to load these files in ChAMP using either champ.import or champ.load function I get the error that pd file does not match with green channel idat file. I am very confused about how to load this excel sheet into champ. I don't even have idat files. Can anyone help me?


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

[ Section 1: Read PD Files Start ]

CSV Directory: E:/new project ideas/march, 2024/data/figures/methylation/analysis/pd.csv

Find CSV Success

Reading CSV File

Replace Sentrix_Position into Array

Replace Sentrix_ID into Slide

Error in champ.import("E:/new project ideas/march, 2024/data/figures/methylation/analysis") :

Error Match between pd file and Green Channel IDAT file.

Thanks a lot! Tahirah


ChAMP • 142 views
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"champ.load() can not perform filtering on beta matrix alone. For users have no .IDAT data but beta matrix and Sample_Sheet.csv, you may want perform filtering using the champ.filter() function and then use following functions to do analysis."

If you have no .idat files but a beta matrix, you should start at the champ.filter() step


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