IlluminaHumanMethylationEPIC array nSNPsRead and MethylSet probes
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@giovanni-calice-6415
Last seen 16 months ago
Italy

Hi all,

I'm processing some new IlluminaHumanMethylationEPIC arrays but I obtained different reading number of SNPs
(nSNPsRead) in the IDAT files, 1051815, compared to the ones I've always usually got from IlluminaHumanMethylationEPIC array, 1052641

.

#
# Old chip file
#
old$nSNPsRead # # 1052641 # # # New chip file # new <- readIDAT("/working_path/202060330128/202060330128_R01C01_Grn.idat") new$nSNPsRead
#
# 1051815
#

I have performed these tests for a single file because then creating the MethylSets I get a smaller number of probes, 866091, compared to what I always got and that identifies the EPIC array, 866836.

Why do not I get the canonical size of the EPIC array from reading the new idat files?

Giovanni


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@kasper-daniel-hansen-2979
Last seen 10 months ago
United States
The number of probes inside an IDAT file depends on the settings of the scanner at the time of the scanning of the file. This is encaptured in a so-called DMAP file. Unfortunately, Illumina has releaed multiple DMAP files for the EPIC chip so it is quite standard to see what you see. This was never really an issue for the 450k array. Best, Kasper On Tue, Jan 9, 2018 at 12:18 PM, Giovanni Calice [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Giovanni Calice <https: support.bioconductor.org="" u="" 6415=""/> wrote Question: > IlluminaHumanMethylationEPIC array nSNPsRead and MethylSet probes > <https: support.bioconductor.org="" p="" 104722=""/>: > > Hi all, > > I'm processing some new IlluminaHumanMethylationEPIC arrays but I obtained > different reading number of SNPs > (nSNPsRead) in the IDAT files, 1051815, compared to the ones I've always > usually got from IlluminaHumanMethylationEPIC array, 1052641 > > . > > # > # Old chip file > # > old <- readIDAT("/working_path/200691450004/200691450004_R03C01_Grn.idat") > old$nSNPsRead > # > # 1052641 > # > # > # New chip file > # > new <- readIDAT("/working_path/202060330128/202060330128_R01C01_Grn.idat") > new$nSNPsRead > # > # 1051815 > # > > I have performed these tests for a single file because then creating the > MethylSets I get a smaller number of probes, 866091, compared to what I > always got and that identifies the EPIC array, 866836. > > Why do not I get the canonical size of the EPIC array from reading the new > idat files? > > > Thanks in advance, > Giovanni > > > > ------------------------------ > > Post tags: illuminaio, illuminahumanmethylationepicmanifest, minfi > > You may reply via email or visit https://support.bioconductor. > org/p/104722/ >
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Dear Kasper,

in fact for the 450k it never happened this issue.

Thanks for response, Best

Giovanni