*Hi BioC list,
**
**In package beadarray, when I do boxplot of raw data,
do I really have to do log2 transformation according
to the example code in the tutorial:
> boxplot(as.data.frame(log2(exprs(BSData))),
+ las = 2, outline = FALSE, ylab = "log2(intensity)")?

The reason I asked this question is because I find some
negative intensity values, which should prevent the log2
transformation.

Another question is that whether there is an option in beadarray
to filter out some probes across samples whose Detection P
value is significantly lower than a threshold.

Thanks a lot for your suggestion!

Alex

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