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

Hi Sunjae, > Is there any possibility to combine, normalize and analyze them without problems? I think the order should be "normalize, combine, and analyze (hopefully) without problems." I don't really see a way (nor a good reason) for combining the different platforms first and then doing the pre-processing. Best regards, --Johannes -----Original Message----- From: ??? [mailto:sjlee@biosoft.kaist.ac.kr] Sent: Tuesday, September 27, 2011 11:05 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] [question] integration of microarray data from different sources in limma package 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 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor