using linear model of limma
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Jianping Jin ▴ 890
@jianping-jin-1212
Last seen 9.6 years ago
Dear list: A batch effect was observed in 16 out of 105 hgU133_plus2 arrays based on NUSE plot. I know SAM, like limma, is able to handle this kind of thing with setting block. But I am not sure if that is appropriate way for this unintentional situation. I would try to use the lmFit function of limma with batch as a factor to remove the batch effect. Then use the resulting data values for other software applications, for example SAM. Here come my questions: 1. Should I apply the raw data, data at exprs, instead of eset at exprs for running lmFit? 2. If that is a right way, how can I extract the lmFit normalized data for next RMA or GCRMA? Please point it out if I am confused with something! I will appreciate your help! Jianping ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu
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Jianping Jin ▴ 890
@jianping-jin-1212
Last seen 9.6 years ago
Dear list, This is a follow-up info to my first email (see below). I tried to use lmFit on my raw data, data at exprs which is a read.affybatch object. I realized that there was no way for me to retrieve the linear model fitted resulting values for next data procession as the results are stored in a compact form as stated in the on-line help document. It looks like that the easier way to handle the chip batch effect for my data is to include "batch" as a factor in the fit model and let limma do the further procession. So the usual processes are reading .CEL files in, preprocessing data with RMA/GCRMA, fitting data with linear model and then using eBayes. I have questions here, please forgive me as a none statistician, if the quantile normalization in RMA would do any harm than good to the data when a batch effect exists? What else does lmFit do if RMA has already removed the batch effect? Please help me out for this confusion. thanks! Jianping --On Wednesday, November 15, 2006 11:50 AM -0500 Jianping Jin <jjin at="" email.unc.edu=""> wrote: > > Dear list: > > A batch effect was observed in 16 out of 105 hgU133_plus2 arrays based on > NUSE plot. I know SAM, like limma, is able to handle this kind of thing > with setting block. But I am not sure if that is appropriate way for this > unintentional situation. > > I would try to use the lmFit function of limma with batch as a factor to > remove the batch effect. Then use the resulting data values for other > software applications, for example SAM. Here come my questions: > 1. Should I apply the raw data, data at exprs, instead of eset at exprs for > running lmFit? > 2. If that is a right way, how can I extract the lmFit normalized data > for next RMA or GCRMA? > > Please point it out if I am confused with something! I will appreciate > your help! > > Jianping > > ################################## > Jianping Jin Ph.D. > Bioinformatics scientist > Center for Bioinformatics > Room 3133 Bioinformatics building > CB# 7104 > University of Chapel Hill > Chapel Hill, NC 27599 > Phone: (919)843-6105 > FAX: (919)843-3103 > E-Mail: jjin at email.unc.edu ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu
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Hi Jianping, >So the usual processes are reading .CEL files in, preprocessing data with >RMA/GCRMA, fitting data with linear model and then using eBayes. I have >questions here, please forgive me as a none statistician, if the quantile >normalization in RMA would do any harm than good to the data when a batch >effect exists? What else does lmFit do if RMA has already removed the batch >effect? In my experience, quantile normalization does not always remove a batch effect. You can test this by using some sort of clustering on the arrays using both the raw data and then the RMA values. I like the 'overview' function in the made4 package, but I have no idea if it will handle 105 arrays. If you're going to fit a batch in limma, you should be using 'duplicateCorrelation', and you can see if the consensus correlation is positive; if it's near zero or negative, then your batch effect isn't large enough overall to worry about. Cheers, Jenny >Please help me out for this confusion. > >thanks! > >Jianping > >--On Wednesday, November 15, 2006 11:50 AM -0500 Jianping Jin ><jjin at="" email.unc.edu=""> wrote: > > > > > Dear list: > > > > A batch effect was observed in 16 out of 105 hgU133_plus2 arrays based on > > NUSE plot. I know SAM, like limma, is able to handle this kind of thing > > with setting block. But I am not sure if that is appropriate way for this > > unintentional situation. > > > > I would try to use the lmFit function of limma with batch as a factor to > > remove the batch effect. Then use the resulting data values for other > > software applications, for example SAM. Here come my questions: > > 1. Should I apply the raw data, data at exprs, instead of eset at exprs for > > running lmFit? > > 2. If that is a right way, how can I extract the lmFit normalized data > > for next RMA or GCRMA? > > > > Please point it out if I am confused with something! I will appreciate > > your help! > > > > Jianping > > > > ################################## > > Jianping Jin Ph.D. > > Bioinformatics scientist > > Center for Bioinformatics > > Room 3133 Bioinformatics building > > CB# 7104 > > University of Chapel Hill > > Chapel Hill, NC 27599 > > Phone: (919)843-6105 > > FAX: (919)843-3103 > > E-Mail: jjin at email.unc.edu > > > >################################## >Jianping Jin Ph.D. >Bioinformatics scientist >Center for Bioinformatics >Room 3133 Bioinformatics building >CB# 7104 >University of Chapel Hill >Chapel Hill, NC 27599 >Phone: (919)843-6105 >FAX: (919)843-3103 >E-Mail: jjin at email.unc.edu > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
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