[BioC] [question] integration of microarray data from different sources in limma package

[이선재]

Dear developers,

I want to ask some questions about microarray data pre-processing

In the limma package, it supports reading microarray data from different
source such as agilent(agilent feature extraction), genepix(genepix pro)
format by fuction read.maimages().

And cbind fuction enables us to combine RGList obtained from micorarray
data from different source

However, when we try to normalize the combined RGList data through
normalizeBetweenArrays function and analyze differentially expressed
gene through lmFit, eBayes function, it produces some problems of
not-compatible integrations due to diffrenence of its sources. ( I just
want to integrate microarray data from agilent and genepix format as
soon as possible )

Is there any possibility to combine, normalize and analyze them without
problems?

please let me know how to solve them.



Sincerely,

Sunjae LEE

Ph.D. candidate, BISL, Dept. of Bio and Brain engineering, KAIST
335-Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea