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ERROR Undefined platform; unexpected or missing IDAT files #32

Open mishraa31 opened 1 year ago

mishraa31 commented 1 year ago

Hi Team, I am using the RnBeads package for analysing Idat files but for some of my files, I am getting an error message of "ERROR Undefined platform; unexpected or missing IDAT files" , though idat files and sample sheet are present in my working directory.I am able to open these idat files in other packages like GenomeStudio and illuminaio.Please find the attached error screenshot for the same. Please let me know how to proceed with this. Command used for the same: rnb.run.analysis(dir.reports=resultDir, sample.sheet=sample.annotation, data.dir=idat.dir, data.type="idat.dir")

Thanks and regards, Aman

schmic05 commented 1 year ago

Hi Aman,

From your description I would speculate that some of the IDAT files in the sample annotation sheet are not present in your IDAT directory. This can happen if you have a typo in the SentrixID/Position, which might also arise from the conversion to scientific numbering that Excel sometimes does. Please validate that all of the files listed in your sample annotation sheet are also present.

Best,

Michael

mishraa31 commented 1 year ago

Hi Michael,

I have checked the IDAT directory and sample annotation files, it seems fine to me. Please find the attached data and annotation file. Could you please look into it and let me know how to proceed with this thing.

Thanks and regards, Aman idat.zip https://drive.google.com/file/d/13mrl1xo2FNkVfOleuHjy6gdOHhuwT-zv/view?usp=drive_web

On Thu, Oct 13, 2022 at 12:42 PM Michael Scherer @.***> wrote:

Hi Aman,

From your description I would speculate that some of the IDAT files in the sample annotation sheet are not present in your IDAT directory. This can happen if you have a typo in the SentrixID/Position, which might also arise from the conversion to scientific numbering that Excel sometimes does. Please validate that all of the files listed in your sample annotation sheet are also present.

Best,

Michael

— Reply to this email directly, view it on GitHub https://github.com/epigen/RnBeads/issues/32#issuecomment-1277133402, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALVDPA6BCIIF5GE5HQ5PZEDWC6Y4PANCNFSM6AAAAAARD4AH5M . You are receiving this because you authored the thread.Message ID: @.***>