illumina beadarray expresion matrix transformation problem

Question

[lovetl2002]

This is my first time dealing with beadarray data. For Affymetrix microarray data, I can easily log-transform it. However for beadarray data, after log-transformation, the shape of the data didn't change too much.

For one single sample,

After log transformation:

So how can I transform the data into normal shape?

[poisonAlien]

Did you normalize before log transformation ? like quantile or spline (RSN) ?

Answer 1

[andrew.j.skelton73]

Have you looked at the lumiT() and lumiN() functions in the lumi package?

Answer 2

[Ying W]

I would highly recommend reading through the manual for beadarray package