[BioC] About between-array normalization in limma

[De-Jian,ZHAO]

Hi,everyone.

I am now analyzing my microarray data using limma. I am not sure
when to use between-array normalization.

In the first case of chapter 11 in limma user's guide, it is
mentioned that between-array normalization is not routine and should
only be done when there is good evidence. I wonder what is a good
evidence and whether I should carry out between-array normalization
in my data. See the attachment for the boxplot.

In the attached boxplot,the blue, red, and green ones stand for
three different hybridization groups. There are 6 replications in
each group. I want to carry out between-array normalization in
the three groups respectively and then combine them together to fit
a linear model. Is this reasonable? In my opinion, we can always
carry out between-array normalization between the replications of
the same hybridization group (unless there is dye swap).

Thanks in advance for your reply.

Dejian Zhao