Hello,

I am using the re-annotation of Illumina probe sequences available in the
 IlluminaMousev2.db (great package!), and I have two questions (please see
code below as well):

1) Is there any difference between Good and Good*** or Perfect and
Perfect**** probe quality?

2) I noticed there are two probes re-annotated to an EntrezID without probe
quality, why would this be?

Thanks!

Lourdes

> library("illuminaMousev2.db")

> x <- illuminaMousev2ENTREZREANNOTATED

> mapped_probes <- mappedkeys(x)

> xx <- as.list(x[mapped_probes])

> probe_EntrezID_re <- unlist(xx)

>

> x <- illuminaMousev2PROBEQUALITY

> mapped_probes <- mappedkeys(x)

> # Convert to a list

> xx <- as.list(x[mapped_probes])

> probe_quality_re <- unlist(xx)

>

> table(probe_quality_re[intersect(names(probe_EntrezID_re),
names(probe_quality_re))])


        Bad        Good     Good***    Good****    No match     Perfect
 Perfect*** Perfect****

       3657         996          38         302          79       31819
   1719        1047

>

> setdiff(names(probe_EntrezID_re), names(probe_quality_re))

[1] "ILMN_1229593" "ILMN_2694153"

> probe_quality_re[c("ILMN_1229593", "ILMN_2694153")]

<NA> <NA>

  NA   NA

>

> sessionInfo()

R version 2.14.1 (2011-12-22)

Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)


locale:

[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8


attached base packages:

[1] grid      stats     graphics  grDevices utils     datasets  methods
base


other attached packages:

 [1] gplots_2.10.1             KernSmooth_2.23-7         caTools_1.12
       bitops_1.0-4.1

 [5] gdata_2.8.2               gtools_2.6.2              limma_3.10.2
       illuminaMousev2.db_1.12.1

 [9] org.Mm.eg.db_2.6.4        RSQLite_0.11.1            DBI_0.2-5
        AnnotationDbi_1.16.15

[13] Biobase_2.14.0            BiocInstaller_1.2.1


loaded via a namespace (and not attached):

[1] IRanges_1.12.6 tools_2.14.1

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