Question

error with champ.load

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jkong • 0

@jkong-23309

Last seen 4.6 years ago

Hi everyone.

I'm using methylation file downloaded from GEO database, and tried to use champ.load to read methylation data (.idat).

However I was getting the following error :

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

I have checked the ChAMP code but was not able to find any ways to correct it.

I also tried loading various versions of csv files but was unsuccessful. I have posted one the the csv files below.

Thank you so much.

Billy

CSV file

[Data],,,,,,, SampleName,SamplePlate,SampleGroup,PoolID,Project,SampleWell,SentrixID,Sentrix_Position HCT8-0h-1,,S,,,,GSM2140588,R01C01 HCT8-0h-2,,S,,,,GSM2140589,R02C01 HCT8-0h-3,,S,,,,GSM2140590,R03C01 HCT8-5Fu-0h-1,,R,,,,GSM2140594,R01C02 HCT8-5Fu-0h-2,,R,,,,GSM2140595,R02C02 HCT8-5Fu-0h-3,,R,,,,GSM2140596,R03C02 HCT8-5Fu-72h-1,,R,,,,GSM2140597,R04C02 HCT8-5Fu-72h-2,,R,,,,GSM2140598,R05C02 HCT8-5Fu-72h-3,,R,,,,GSM2140599,R06C02

ChAMP champ methylation • 2.3k views

ADD COMMENT • link updated 15 months ago by mike • 0 • written 4.6 years ago by jkong • 0

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Hi:

Is that "SentrixID" in your csv file? Could you try replace it with "Sentrix_ID", then retry?

Best Tian

ADD REPLY • link 4.6 years ago Yuan Tian ▴ 290

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Hi Thank you for your reply.

I have tried replacing it to "Sentrix_ID", but still getting the same error.

I'm just curious if 'champ.import' can take file format other than 'csv' files.

Again, thank you so much for your help.

ADD REPLY • link 4.6 years ago jkong • 0

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Hi:

Your CSV file still looks have some problem, because it does not contain the array information.

You should have the access to my demo data in your computer. Open R, type:

testDir=system.file("extdata",package="ChAMPdata")

Then the testDir is the directory where Demo data it, you can cd into the folder, then you can find a csv file in it. There should be a column with very long number. Seems I did not see it in your csv file.

Best Tian

ADD REPLY • link 4.6 years ago Yuan Tian ▴ 290

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Hi

Correcting the array information solved the problem.

Thank you so much for your help!

Best Billy

ADD REPLY • link 4.6 years ago jkong • 0

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Hi,

Can I know how exactly you corrected the array information?

Best Tian

ADD REPLY • link 4.6 years ago Yuan Tian ▴ 290

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Hi, I am also facing error in champ.load

My file is given below:

Sample_Name Sample_Well Sample_Plate Sample_Group Sample_ID Pool_ID Sentrix_ID Sentrix_Position C11 T 304972 2.04E+11 R03C01 C19 T 304981 2.04E+11 R04C01 C22 T 304982 2.04E+11 R05C01 C48-R T 342585 2.04E+11 R05C01 CD1 C 360772 2.04E+11 R04C01 CD2 C 342601 2.04E+11 R05C01

Error Section 1: Read PD Files Start ] CSV Directory: /home/amit/@nidhi-Methy-Cluster1//sample_sheet.csv Find CSV Success Reading CSV File Replace Sentrix_Position into Array Replace Sentrix_ID into Slide Error in champ.import(directory, arraytype = arraytype) : Error Match between pd file and Green Channel IDAT file.

Please guide me. Thank you so much

ADD REPLY • link 3.3 years ago Nidhi • 0

score 0 · Answer 1 · 2023-08-17

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