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Dear all, we are planning to perform methylation profiling of FFPE tumor samples with the Infinium MetlylationEPIC v2.0 chips, and we would like to use the data to do CNV analysis as well. Can conumee be run on data generated on this type of chip? If not natively, is there a way to make the package run on those data? Thank you for the help. Luca
Hi Luca, could you give conumee2 a try? https://github.com/bjarnedae/conumee-2
Since the vignette is not updated yet, I send you some instructions to use CNV.import function to import EPICv2 idat files:
Sole
Hi,
First thank you for this adaptation of conumee. My colleagues and me get a brand new NextSeq 550 with EPICv2 array. So I've tried conumee2.0, but I got an error message:
CNV.import(array_type = "EPICv2", directory = ".", sample_sheet = "Demo_EPIC-8v2-0_A1_NextSeq550_SampleSheet_3.csv")
Error in (function (classes, fdef, mtable) : impossible de trouver une methode heritee pour la fonction CNV.import pour la signature "character", "character", "character" I would be grateful for your help.
Best regards.
PS: this message is also posted in GitHub as an issue (https://github.com/bjarnedae/conumee-2/issues/1)
Hi!
This issue has been answered on GitHub (https://github.com/bjarnedae/conumee-2/issues/1) by the owner of the conumee2.0 package .
Best regards,
Sole
Hi Sole,
If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create annotation object of 450K, EPIC, EPICv2 and overlap, and it stills give me this error:
Error in .local(query, ref, anno, ...) : query intensities not given for all probes.
Best Regards, Max
Hi Max,
Could you try this?
conumee (for EPIC): query intensities not given for all probes
Hello,
I had similar issue with conumee 2.0 for EPICv2 array. I tried to create anno from overlap and processed idats with cnv.import & cnv.load. And I tried anno@probes <- anno@probes[names(anno@probes) %in% names(minfi::getLocations(IlluminaHumanMethylationEPICanno.ilm10b4.hg19::IlluminaHumanMethylationEPICanno.ilm10b4.hg19))]
But I have the same issue of error of :query intensities not given for all probes
Please suggest. Thank you.
Actually after mapping the probes between annotation and data, I am able to run cnv.fit. But it is running into error on segment function. The error is seen below. Is there any way I can filter probes with zero weights.
Error in if (min(weights) <= 0) stop("all weights should be positive") : missing value where TRUE/FALSE needed
Thanks in advance.
I had the same issue, did anyone find a solution? Could the issue be with DNAcopy?
i also have the same issue, if anyone managed to find a solution it would be great if you could share it! (EPICv2 samples + conumee2 (not conumee 2.0)