Question: Error with IlluminaHumanMethylation450Kmanifest when trying to run ChAMP
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gravatar for bohao.liu
3.4 years ago by
bohao.liu0
bohao.liu0 wrote:

Hi,

I've been trying to get the ChAMP package to run and right now when I try to run champ.load, I get an error saying "cannot open file '~/R/win-library/3.3/IlluminaHumanMethylation450kmanifest/data/Rdata.rdb': No such file or directory".  I have the packaged installed and the file is definitely there, so I am not sure why this error is occurring.  I've been able to get ChAMP to work for another set of EPIC data that I have using the EPIC manifest so I'm confused why it doesn't work with the 450K manifest.  Thanks in advance for the help.

 

 

ADD COMMENTlink modified 3.4 years ago by chaoqiang.lai0 • written 3.4 years ago by bohao.liu0
Answer: Error with IlluminaHumanMethylation450Kmanifest when trying to run ChAMP
0
gravatar for chaoqiang.lai
3.4 years ago by
chaoqiang.lai0 wrote:

There is one possibility that gives such an error - please check your sample_sheet.csv file, and make sure the values of "Sentrix_ID" column matching the first number of the idat file name in the folder. Because the digits (barcode number) of the "Sentrix_ID"  are so long,  they could be in a "scientific" format before you save it as a .csv file. Hence, the values of "Sentrix_ID" may be no longer the same number as the first number of the  idat file name.

ADD COMMENTlink written 3.4 years ago by chaoqiang.lai0
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