Error in loading file using champ.load() from ChAMP package
Entering edit mode
arisarkar88 ▴ 40
Last seen 7 months ago
Los Angeles

Hello, I am trying to load .idat files in ChAMP using champ.load(). However I get the following error:

Your pd file contains NO Array(Sentrix_Position) information.

Your pd file contains NO Slide(Sentrix_ID) information.

Error in champ.import(directory, arraytype = arraytype) :

Error Match between pd file and Green Channel IDAT file.

Here is my code:

myLoad <- champ.load("my_dir")

I do have the 'Array' and 'Slide' columns in the samplesheet but it still gives me the error. Here is my samplesheet:

Sample_Name Sample_Plate    Sample_Group    Pool_ID Project Sample_Well Array   Slide   Basename    filenames
C1  C1  NA  C   NA  NA  E01 R05C01  2.03839E+11 203839170007_R05C01 203839170007_R05C01
C2  C2  NA  C   NA  NA  H01 R08C01  2.03839E+11 203839170007_R08C01 203839170007_R08C01
C3  C3  NA  C   NA  NA  C02 R03C01  2.03839E+11 203839170008_R03C01 203839170008_R03C01
T1  T1  NA  T   NA  NA  D01 R04C01  2.03839E+11 203839170007_R04C01 203839170007_R04C01
T2  T2  NA  T   NA  NA  G01 R07C01  2.03839E+11 203839170007_R07C01 203839170007_R07C01 
T3  T3  NA  T   NA  NA  B02 R02C01  2.03839E+11 203839170008_R02C01 203839170008_R02C01 
champ.load epicarray ChAMP methylationArrayAnalysis • 889 views
Entering edit mode
Last seen 2 days ago
United States

The error

Error Match between pd file and Green Channel IDAT file.

Is telling you that the green channel IDAT files don't match with what is in your pd file. You'll have to inspect the contents of your BaseName directory to see what the problem is.

Entering edit mode

I solved the error! I checked the pd file and the Green Channel IDAT file. They look fine and are matched. There was a problem in the sample sheet file format and R was unable to read the numeric columns. It works now. Thanks for your help!


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