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

[이선재]

Hi Johannes,

I would like to explain my data in detail for your deep understanding.
There are three replicate data from two-channel microarray

Two of them were scanned by genepix scanner and the other was scanned by
agilent scanner.

All of them are originated from same microarray platform( agilent chip
). Just different scanner makes them provide different outputs, but its
original information is same.

However, when I want to use three microarray data for the analysis using
limma package, it is difficult to use built-in functions in the package
to normalize and analyze them for extracting DEGs(differentially
expressed genes).

For example,

library(limma)
setwd("~~")
targets_agilent = readTargets("targets_agilent.txt")
targets_genepix = readTargets("targets_genepix.txt")
rg_agilent = read.maimages(targets_agilent$FileName, source="agilent")
rg_genepix = read.maimages(targets_genepix$FileName, source="genepix")
rg_all = cbind( rg_agilent, rg_genepix )

When I tried to use rg_all object for further analysis, it provokes some
problems because cbind function just concetanates the data without
consideration of interal information.

Please let me know your precious opinion for this beginner in this field.

Thanks in advance.

Sincerely,

Sunjae LEE




2011-10-01 오전 2:29, Freudenberg, Johannes (NIH/NIEHS) [E] 쓴 글:
> 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: 이선재 [mailto:sjlee at 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
>
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-- 
Sunjae LEE
Ph.D. candidate, BISL, Dept. of Bio and Brain engineering, KAIST
335-Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea
TEL +82-42-350-4353
(cell.) +82-10-3090-9050