[BioC] affyPLM QC

[Tan, Ruimin]

Hi,

I have three same sample running on the Affy test3 chip. I would like to
check if the data is consistency. I run affyPLM package. I test results
of RLE and NUSE. The results as follows:

RLE(Pset,type ="stats")
       QCtest1.CEL QCtest2.CEL
median  0.00000000  0.00000000
IQR     0.04745306  0.07492608
       QCtest3.CEL
median  0.00000000
IQR     0.07739142
> NUSE(Pset, type ="stats")
       QCtest1.CEL QCtest2.CEL
median  1.00000000  1.00000000
IQR     0.02190403  0.01405276
       QCtest3.CEL
median  1.00000000
IQR     0.01762973

Attached is the image of RLE and NUSE box plot. In fact, the box plot
confused me. Some box on the top of the median line. What is the
problem? Any input is appropriated.

Terry.