How to get and save normalized data from limma

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Wang, Jixin ▴ 130

@wang-jixin-2828

Last seen 9.6 years ago

Dear All, I want to use the normalized signal intensities data to do hierarchical clustering. But I don?t know how to save the normalized data from LIMMA. Below is the code: library(limma) setwd("C:/Documents and Settings/JWang/Desktop/analysis with R/RAO") targets <- readTargets("equi.txt") targets RG <- read.maimages(targets$FileName, source="genepix") RG MA <- normalizeWithinArrays(RG) MA <- normalizeBetweenArrays(MA,method="scale") design <- c(-1,1,-1,1,-1,1) fit <- lmFit(MA,design) fit <- eBayes(fit) topTable(fit,number=500,adjust="BH") volcanoplot(fit) Thanks a lot, Jixin

Clustering limma Clustering limma • 2.7k views

ADD COMMENT • link 15.6 years ago Wang, Jixin ▴ 130

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Wang, Jixin ▴ 130

@wang-jixin-2828

Last seen 9.6 years ago

Hi Mark, Thank you very much for your kind reply. I want to get normalized cy3 and cy5 channel data and tend to look at the correlation (scatter plot) of normalized data between biological replicates and dye swaps. But I can?t figure out R code for this task. I will use MeV(TM4) and Cluster/TreeView software to do the clustering. Here is my target file: SlideNumber FileName Cy3 Cy5 Date 13845971 13845971.gpr R wild type 8/12/2008 13845972 13845972.gpr wild type R 8/12/2008 13845392 13845392.gpr R wild type 8/12/2008 13845393 13845393.gpr wild type R 8/12/2008 13845400 13845400.gpr R wild type 8/12/2008 13845401 13845401.gpr wild type R 8/12/2008 Regards, Jixin ----- Original Message ----- From: "Mark Robinson" <mrobinson@wehi.edu.au> To: "Jixin Wang" <jixinwang at="" neo.tamu.edu=""> Cc: bioconductor at stat.math.ethz.ch Sent: Wednesday, September 10, 2008 5:00:23 PM GMT -06:00 US/Canada Central Subject: Re: [BioC] How to get and save normalized data from limma Jixin. I believe you want the normalized log-ratios, which are stored in MA$M. For example: library(gplots) heatmap.2(MA$M) ... of course, depending on the number of rows in your data, you may want to take a subset ... HTH, Mark On 11/09/2008, at 6:27 AM, Wang, Jixin wrote: > Dear All, > > I want to use the normalized signal intensities data to do > hierarchical clustering. But I don?t know how to save the normalized > data from LIMMA. > > > Below is the code: > > library(limma) > setwd("C:/Documents and Settings/JWang/Desktop/analysis with R/RAO") > targets <- readTargets("equi.txt") > targets > RG <- read.maimages(targets$FileName, source="genepix") > RG > > MA <- normalizeWithinArrays(RG) > > MA <- normalizeBetweenArrays(MA,method="scale") > > design <- c(-1,1,-1,1,-1,1) > fit <- lmFit(MA,design) > > > fit <- eBayes(fit) > topTable(fit,number=500,adjust="BH") > > volcanoplot(fit) > > Thanks a lot, > > Jixin > > _______________________________________________ > 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 ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 _______________________________________________ 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

ADD COMMENT • link 15.6 years ago Wang, Jixin ▴ 130

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Hi Jixin, So you have 6 arrays, and thus 12 channels of data. Do you want a heatmap of the 12 columns of red and green? If so, have a look at ?RG.MA in limma. Do you want a heatmap of the 6 sets of log ratios of Red vs Green on each array? If so they're in MA$M cheers, Mark On 11/09/2008, at 12:56 PM, Wang, Jixin wrote: > Hi Mark, > Thank you very much for your kind reply. > > I want to get normalized cy3 and cy5 channel data and tend to look > at the correlation (scatter plot) of normalized data between > biological replicates and dye swaps. But I can?t figure out R code > for this task. I will use MeV(TM4) and Cluster/TreeView software to > do the clustering. > > Here is my target file: > > SlideNumber FileName Cy3 Cy5 Date > 13845971 13845971.gpr R wild type 8/12/2008 > 13845972 13845972.gpr wild type R 8/12/2008 > 13845392 13845392.gpr R wild type 8/12/2008 > 13845393 13845393.gpr wild type R 8/12/2008 > 13845400 13845400.gpr R wild type 8/12/2008 > 13845401 13845401.gpr wild type R 8/12/2008 > > > Regards, > > Jixin > > ----- Original Message ----- > From: "Mark Robinson" <mrobinson at="" wehi.edu.au=""> > To: "Jixin Wang" <jixinwang at="" neo.tamu.edu=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Wednesday, September 10, 2008 5:00:23 PM GMT -06:00 US/Canada > Central > Subject: Re: [BioC] How to get and save normalized data from limma > > Jixin. > > I believe you want the normalized log-ratios, which are stored in MA > $M. > > For example: > > library(gplots) > heatmap.2(MA$M) > > ... of course, depending on the number of rows in your data, you may > want to take a subset ... > > HTH, > Mark > > On 11/09/2008, at 6:27 AM, Wang, Jixin wrote: > >> Dear All, >> >> I want to use the normalized signal intensities data to do >> hierarchical clustering. But I don?t know how to save the normalized >> data from LIMMA. >> >> >> Below is the code: >> >> library(limma) >> setwd("C:/Documents and Settings/JWang/Desktop/analysis with R/RAO") >> targets <- readTargets("equi.txt") >> targets >> RG <- read.maimages(targets$FileName, source="genepix") >> RG >> >> MA <- normalizeWithinArrays(RG) >> >> MA <- normalizeBetweenArrays(MA,method="scale") >> >> design <- c(-1,1,-1,1,-1,1) >> fit <- lmFit(MA,design) >> >> >> fit <- eBayes(fit) >> topTable(fit,number=500,adjust="BH") >> >> volcanoplot(fit) >> >> Thanks a lot, >> >> Jixin >> >> _______________________________________________ >> 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 > > ------------------------------ > Mark Robinson > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: m.robinson at garvan.org.au > e: mrobinson at wehi.edu.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > > _______________________________________________ > 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 > > _______________________________________________ > 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 ----------------------------------------------------- Mark Cowley, BSc (Bioinformatics)(Hons) Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia

ADD REPLY • link 15.6 years ago Mark Cowley ▴ 910

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Hi Mark, Thank you so much for your kind help! I got it. Best Regards, Jixin ----- Original Message ----- From: "Mark Cowley" <m.cowley@garvan.org.au> To: "Jixin Wang" <jixinwang at="" neo.tamu.edu=""> Cc: bioconductor at stat.math.ethz.ch Sent: Wednesday, September 10, 2008 11:39:16 PM GMT -06:00 US/Canada Central Subject: Re: [BioC] How to get and save normalized data from limma Hi Jixin, So you have 6 arrays, and thus 12 channels of data. Do you want a heatmap of the 12 columns of red and green? If so, have a look at ?RG.MA in limma. Do you want a heatmap of the 6 sets of log ratios of Red vs Green on each array? If so they're in MA$M cheers, Mark On 11/09/2008, at 12:56 PM, Wang, Jixin wrote: > Hi Mark, > Thank you very much for your kind reply. > > I want to get normalized cy3 and cy5 channel data and tend to look > at the correlation (scatter plot) of normalized data between > biological replicates and dye swaps. But I can?t figure out R code > for this task. I will use MeV(TM4) and Cluster/TreeView software to > do the clustering. > > Here is my target file: > > SlideNumber FileName Cy3 Cy5 Date > 13845971 13845971.gpr R wild type 8/12/2008 > 13845972 13845972.gpr wild type R 8/12/2008 > 13845392 13845392.gpr R wild type 8/12/2008 > 13845393 13845393.gpr wild type R 8/12/2008 > 13845400 13845400.gpr R wild type 8/12/2008 > 13845401 13845401.gpr wild type R 8/12/2008 > > > Regards, > > Jixin > > ----- Original Message ----- > From: "Mark Robinson" <mrobinson at="" wehi.edu.au=""> > To: "Jixin Wang" <jixinwang at="" neo.tamu.edu=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Wednesday, September 10, 2008 5:00:23 PM GMT -06:00 US/Canada > Central > Subject: Re: [BioC] How to get and save normalized data from limma > > Jixin. > > I believe you want the normalized log-ratios, which are stored in MA > $M. > > For example: > > library(gplots) > heatmap.2(MA$M) > > ... of course, depending on the number of rows in your data, you may > want to take a subset ... > > HTH, > Mark > > On 11/09/2008, at 6:27 AM, Wang, Jixin wrote: > >> Dear All, >> >> I want to use the normalized signal intensities data to do >> hierarchical clustering. But I don?t know how to save the normalized >> data from LIMMA. >> >> >> Below is the code: >> >> library(limma) >> setwd("C:/Documents and Settings/JWang/Desktop/analysis with R/RAO") >> targets <- readTargets("equi.txt") >> targets >> RG <- read.maimages(targets$FileName, source="genepix") >> RG >> >> MA <- normalizeWithinArrays(RG) >> >> MA <- normalizeBetweenArrays(MA,method="scale") >> >> design <- c(-1,1,-1,1,-1,1) >> fit <- lmFit(MA,design) >> >> >> fit <- eBayes(fit) >> topTable(fit,number=500,adjust="BH") >> >> volcanoplot(fit) >> >> Thanks a lot, >> >> Jixin >> >> _______________________________________________ >> 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 > > ------------------------------ > Mark Robinson > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: m.robinson at garvan.org.au > e: mrobinson at wehi.edu.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > > _______________________________________________ > 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 > > _______________________________________________ > 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 ----------------------------------------------------- Mark Cowley, BSc (Bioinformatics)(Hons) Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia _______________________________________________ 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

ADD REPLY • link 15.6 years ago Wang, Jixin ▴ 130

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Mark Robinson ★ 1.1k

@mark-robinson-2171

Last seen 9.6 years ago

Jixin. I believe you want the normalized log-ratios, which are stored in MA$M. For example: library(gplots) heatmap.2(MA$M) ... of course, depending on the number of rows in your data, you may want to take a subset ... HTH, Mark On 11/09/2008, at 6:27 AM, Wang, Jixin wrote: > Dear All, > > I want to use the normalized signal intensities data to do > hierarchical clustering. But I don?t know how to save the normalized > data from LIMMA. > > > Below is the code: > > library(limma) > setwd("C:/Documents and Settings/JWang/Desktop/analysis with R/RAO") > targets <- readTargets("equi.txt") > targets > RG <- read.maimages(targets$FileName, source="genepix") > RG > > MA <- normalizeWithinArrays(RG) > > MA <- normalizeBetweenArrays(MA,method="scale") > > design <- c(-1,1,-1,1,-1,1) > fit <- lmFit(MA,design) > > > fit <- eBayes(fit) > topTable(fit,number=500,adjust="BH") > > volcanoplot(fit) > > Thanks a lot, > > Jixin > > _______________________________________________ > 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 ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852

ADD COMMENT • link 15.6 years ago Mark Robinson ★ 1.1k

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