conumee with Infinium MethylationEPIC v2.0
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Maximus • 0
@3cb8d044
Last seen 8 weeks ago
Hong Kong

I tried to perform CNV analysis using conumee 2.0 package. Most of the newly analyzed tumour samples are from EPIC2.0, but I want to use the normal control samples from DKFZ reference cohort, which is using EPIC or 450K. I combine MSet generated from EPICv2, EPIC and 450K array using the CombineArray() function from minfi. I tried different options of generating annotation, but when I try to CNV.fit(minfi.data["GLI1"], minfi.data[minfi.controls], anno), it just outputs Error in .local(query, ref, anno, ...) : query intensities not given for all probes.

Is there a step-by-step tutorial as to how to combine the new EPICv2 data with public data using EPICv1 and 450K, and generating annotation file that can run the conumee2.0?

Thanks.

Best Regards,

Max


control_names <- c("Control (muscle tissue)","Control (reactive tissue)", "Control (blood)")

##Different options of generating annotation

anno_overlap <- CNV.create_anno(bin_minprobes = 15, bin_minsize = 50000,
                         bin_maxsize = 5000000, array_type = "overlap", chrXY = FALSE,
                         exclude_regions = exclude_regions, detail_regions = detail_regions)
anno_450k <- CNV.create_anno(bin_minprobes = 15, bin_minsize = 50000,
                         bin_maxsize = 5000000, array_type = "450k", chrXY = FALSE,
                         exclude_regions = exclude_regions, detail_regions = detail_regions)

anno_EPIC <- CNV.create_anno(bin_minprobes = 15, bin_minsize = 50000,
                               bin_maxsize = 5000000, array_type = "EPIC", chrXY = FALSE,
                               exclude_regions = exclude_regions, detail_regions = detail_regions)

anno_EPICv2 <- CNV.create_anno(bin_minprobes = 15, bin_minsize = 50000,
                               bin_maxsize = 5000000, array_type = "EPICv2", chrXY = FALSE,
                               exclude_regions = exclude_regions, detail_regions = detail_regions)

#Load MSet data
minfi.data <- CNV.load(MSet_DKFZ, names = phenoData_DKFZ$ID)

minfi.controls <- phenoData_DKFZ$Diagnosis %in% control_names

##Fit CNV
x <- CNV.fit(minfi.data["GLI1"], minfi.data[minfi.controls], anno_EPIC)
Error in .local(query, ref, anno, ...) : query intensities not given for all probes.
conumee • 212 views
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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.

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