User: Ellen O

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Ellen O0
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Posts by Ellen O

<prev • 7 results • page 1 of 1 • next >
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Error when changing the database for minfi dropLociWithSnps
... I am currently filtering Illumina MethylationEPIC data with minfi, which has run smoothly so far. To remove polymorphic CpGs and SBEs I use the following code: NormFlt <- dropLociWithSnps(NormFlt, snps=c("SBE","CpG"), snpAnno="SNPs.147CommonSingle") And get the following error: Error in getS ...
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Comment: C: DMRcate results file ordered by genomic location and not Stouffer p-val?
... Thanks very much, Tim! ...
written 2.5 years ago by Ellen O0
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DMRcate results file ordered by genomic location and not Stouffer p-val?
... I am following a published workflow on methylation analysis and am currently looking at differentially methylated regions with dmrcate. My results come back ordered by chromosomal region, but I understand that by default they should be ordered by the Stouffer p-value? I have tried to sort the data b ...
methylation dmrcate written 2.5 years ago by Ellen O0 • updated 2.5 years ago by Tim Peters80
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Comment: C: Illumina methylationEPIC demo data in IDAT format?
... Thanks Guido! ...
written 2.6 years ago by Ellen O0
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Illumina methylationEPIC demo data in IDAT format?
... Does anyone know of an available data set for the Illumina EPIC/ 850k array that has files in IDAT format that one can download? I am testing a pipeline before I get my own data back and would like to start with the raw files. Illumina's demo data only has three samples and I would like to test out ...
illumina methylation idat epic methylationepic written 2.6 years ago by Ellen O0 • updated 2.6 years ago by Guido Hooiveld2.5k
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Comment: C: Assessing DMRs between treatment groups: subtracting control group DMRs to accou
... Thanks Aaron! ...
written 2.7 years ago by Ellen O0
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Assessing DMRs between treatment groups: subtracting control group DMRs to account for "baseline" methylation
... I am currently awaiting Illumina methylationEPIC (850k) data and in the mean time figuring out how to assess DMRs with demo data. I am new to these analyses but I am making use of the Maksimovic et al. cross-package workflow (https://f1000research.com/articles/5-1281/v2), which I have found very use ...
limma minfi dmr analysis dmr illumina methylationepic 450k written 2.7 years ago by Ellen O0 • updated 2.7 years ago by Aaron Lun25k

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