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Guest User ★ 12k@guest-user-4897
Last seen 7.0 years ago
Hi All, I am using crlmm package to load Affymetrix SNP6.0 genotype data. crlmmResult[['SNR']] can be used as the quality of arrays and the value less than 5 is of low quality and should be removed from further analysis. I am wondering how to use the confs(crlmmResult), or, what is the threshold of confs for dropping out markers? Thanks! -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  genomewidesnp6Crlmm_1.0.7 crlmm_1.16.9  preprocessCore_1.20.0 oligoClasses_1.20.0  BiocGenerics_0.4.0 loaded via a namespace (and not attached):  AnnotationDbi_1.20.5 Biobase_2.18.0 BiocInstaller_1.8.3  Biostrings_2.26.2 DBI_0.2-5 GenomicRanges_1.10.6  IRanges_1.16.4 Matrix_1.0-9 RSQLite_0.11.2  RcppEigen_0.3.1.2.1 XML_3.95-0.1 affyio_1.26.0  annotate_1.36.0 bit_1.1-9 codetools_0.2-8  ellipse_0.3-7 ff_2.2-10 foreach_1.4.0  genefilter_1.40.0 grid_2.15.2 iterators_1.0.6  lattice_0.20-10 mvtnorm_0.9-9994 parallel_2.15.2  splines_2.15.2 stats4_2.15.2 survival_2.36-14  tools_2.15.2 xtable_1.7-1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.