[BioC] how to use the confs value in crlmm

Shrek [guest] guest at bioconductor.org
Mon Mar 4 05:13:56 CET 2013

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?

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)

[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] genomewidesnp6Crlmm_1.0.7 crlmm_1.16.9
[3] preprocessCore_1.20.0     oligoClasses_1.20.0
[5] BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.20.5 Biobase_2.18.0       BiocInstaller_1.8.3
 [4] Biostrings_2.26.2    DBI_0.2-5            GenomicRanges_1.10.6
 [7] IRanges_1.16.4       Matrix_1.0-9         RSQLite_0.11.2
[10] RcppEigen_0.  XML_3.95-0.1         affyio_1.26.0
[13] annotate_1.36.0      bit_1.1-9            codetools_0.2-8
[16] ellipse_0.3-7        ff_2.2-10            foreach_1.4.0
[19] genefilter_1.40.0    grid_2.15.2          iterators_1.0.6
[22] lattice_0.20-10      mvtnorm_0.9-9994     parallel_2.15.2
[25] splines_2.15.2       stats4_2.15.2        survival_2.36-14
[28] tools_2.15.2         xtable_1.7-1         zlibbioc_1.4.0

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