wateRmelon

[…] got after simple preprocessing and is easier to access. both file formats can be handled by r packages: *.idat files can be read by illuminaio package [] and *.txt files can be dealt with minfi [], watermelon [] et al. we use three datasets for expounding our framework., dataset 1: illumina 450k dataset from dedeurwaerder et al. (geo accession number: gse29290) []. three samples on hct116wt […]

[…] rate (fdr)., methylation was assayed using the illumina 450k beadchip. data were parsed and qced using champ; the probe beta values were quantile-normalized using the ‘dasen’ method from the watermelon package. differential methylation on 425,694 probes post-qc was tested using the cpgassoc package, applying a linear model for tissue status at each probe, with individual id […]

[…] polymer-coated chips were image processed in the illumina’s iscan scanner., data were extracted using methylation module of genomestudio v1.0 software and processed using the “minfi” and “watermelon” packages in r [, ]. raw data was trimmed of probes failing quality assessment, followed by scale-based data correction for illumina type i relative to type ii probes. methylated […]

[…] infinium humanmethylation450k beadchip., quality control (qc) and all statistical analyses were performed using the r version 3.2.5 statistical analysis software [], and the r-packages minfi [], watermelon [], enmix [], sva [], limma [], and mediation []., methylation intensity signals were extracted from raw intensity data using the preprocessenmix procedure []. this includes background […]

[…] ). after the methylation intensity data (idat) files were downloaded from their secure server, we conducted probe filtering, background correction and adjustment for probe types using the methylumi, watermelon and fdb.infiniummethylation.hg19 r packages (pidsley et al., ; triche, ; davis et al., ). quality control was performed on the sample and probe levels with all values for cg05575921 […]

[…] got after simple preprocessing and is easier to access. both file formats can be handled by r packages: *.idat files can be read by illuminaio package [] and *.txt files can be dealt with minfi [], watermelon [] et al. we use three datasets for expounding our framework., dataset 1: illumina 450k dataset from dedeurwaerder et al. (geo accession number: gse29290) []. three samples on hct116wt […]

[…] probes on the x and y chromosomes separately to confirm reported gender; 6) comparing genotype data for up to 65 snp probes on the 450 k array with snp array data; 7) using the pfilter() function in watermelon [] to exclude samples with more than 1% of probes characterized by a detection p value > 0.05, in addition to probes characterized by > 1% of samples having a detection p value > 0 […]

[…] from analysis (n = 24,591), as recommended by the manufacturer. subsequently, data were normalized using the beta-mixture quantile (bmiq) normalization methodology []. this was performed using the watermelon package (version 1.11.0) in r (version 3.2.3; the r project for statistical computing) []. probes that represent known single nucleotide polymorphisms (snps) (n = 84,124) and probes […]