Hello, dear list:

I recently had questions about Illumina data two months ago because of
a large portion of negative values found. Suggested by some expertises
here, I requested our microarray facility to re-process the data by not
doing
any global or background subtraction etc. This way, in deed, there is no
negative values existing. But very surprisingly, by applying two packages,
Lumi and Beadarray respectively, after normalization, the fold change
between the test and normal samples is around 1. Apparently, it should
not be this case. Can anybody here offer some possible reasons for this?

Thank you very much for your help in advance!

Sincerely,
     Allen
<bioconductor@stat.math.ethz.ch>

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