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Entering edit mode
@ogiannakopoulou-13991
Last seen 3.0 years ago

Hello,

I'm using the champ.load to read and filter my data and it works well. However when I want to proceed with the champ.QC I receive an error because the column "Sample_Group" in the csv file provided is empty.

So I tried to add the information of that column ("first" or "second") and use the modified csv file to load the idat files. However at that point I'm getting the following error:

"Error in champ.import(directory, arraytype = arraytype) : Error Match between pd file and Green Channel IDAT file."

I went through the pipeline to check how ChAMP imports the data but I did not manage to pick which is the mistake. I know It would be great if you could help so that I can include this information and proceed with champ.QC.

Thank you,

Olga Giannakopoulou

champ • 3.6k views
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Entering edit mode
Yuan Tian ▴ 250
@yuan-tian-13904
Last seen 17 months ago
United Kingdom

Hello Olga:

Firstly, champ.QC() failed because of lacing of Sample_Group column, which could because your csv file does not contain Sample_Group. That's OK because different research have different column name on most interested covariates. In champ.QC() there should be a parameter called "pheno", you just need to change it as myLoad$pd$your_phenotype, then it should be good.

Based on my experience, the most possible error is because you used Excel to open original CSV file, then added information on that, then same it as CSV again. By doing this, original Sentrix_ID (a very long number) could be changed. I guess it's some format problem with Excel.

Than after you modify the file, ChAMP will load your csv file, then get Sentrix_ID and Sentrix_Position, and map them to IDAT data, since Sentrix_ID has changed, no IDAT file would be matched.

I think this is the most possible reason. Please check you modified CSV file and original one, focus on the Sentrix_ID column.

If not this reason, I would check closer into code.

Best

Yuan Tian

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Entering edit mode

Indeed the problem was with editing the excel file. As you guessed, when I was saving the csv file, after adding Sample_Group information, the Sentrix_ID was changing. I managed to make it work after making sure that Sentrix_ID was in "Numeric" format each time.

Thank you again for the help

Best wishes,

Olga

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Entering edit mode

Firstly i'm a beginner. i have the same problem when I use champ.load("Error Match between pd file and Green Channel IDAT file"). my sample_ sheet is edited using excel by myself. but i don't know how to make sure that Sentrix_ID was in "Numeric" format.

thank you, may

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Entering edit mode

Before editing the excel sheet (adding sample group data) press ctrl+1, then under "category" see that "NUMBER" is pressed. then press F2 and "ENTER". now enter your'e sample group data, save and "champ.load()". this way you can make sure that "sentrix_ID" stays "NUMERIC". Roi Horwitz

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Entering edit mode
Roi • 0
@c837bf67
Last seen 9 weeks ago
Israel

Before editing the excel sheet (adding sample group data) press ctrl+1, then under "category" see that "NUMBER" is pressed. then press F2 and "ENTER". now enter your'e sample group data, save and "champ.load()". this way you can make sure that "sentrix_ID" stays "NUMERIC". Roi Horwitz

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