[BioC] how to use the confs value in crlmm

[Benilton Carvalho]

My recommendation is to define a (quantilic) threshold and filter upon that...

For example, if your preference is to remove the 1% "worse" calls for
your samples:

theCalls = calls(crlmmResult)
theConfs = confs(crlmmResult)
## identify calls for which the confidence scores
## are smaller than the 1%-quantile, and ignore them
thresholds = apply(theConfs, 2, quantile, 0.01)
ignore = sweep(theConfs, 2, thresholds, '-') < 0
theCalls[ignore] = NA

benilton


2013/3/4 Shrek [guest] <guest at bioconductor.org>:
>
> 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:
> [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_0.3.1.2.1  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
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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