error with champ.load
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jkong • 0
@jkong-23309
Last seen 14 months 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 • 202 views
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Hi:

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

Best Tian

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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.

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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

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Hi

Correcting the array information solved the problem.

Thank you so much for your help!

Best Billy

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Hi,

Can I know how exactly you corrected the array information?

Best Tian

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