RG.MA in limma
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Wang, Jixin ▴ 90
@wang-jixin-3327
Last seen 10.2 years ago
Dear All, I have one question that has perplexed me for a while. I use two color arrays and I want to get the normalized log2 intensity values instead of M values in MA$M (say, I have four arrays and I want to get eight channels (red and green) of normalized expression data. How can I get them? I have checked the RG.MA function in R and have confused about this problem. I always got error messages whenever I try. Any help will be greatly appreciated! In R help for package limma, it said MA.RG converts an unlogged RGList object into an MAList object. MA.RG(object) is equivalent to normalizeWithinArrays(object,method="none"). RG.MA(object) converts back from an MAList object to a RGList object with unlogged intensities. > RG.MA$R <- 2^(MA$A + MA$M/2) Error in RG.MA$R <- 2^(MA$A + MA$M/2) : object of type 'closure' is not subsettable > RG.MA$G <- 2^(MA$A - MA$M/2) Error in RG.MA$G <- 2^(MA$A - MA$M/2) : object of type 'closure' is not subsettable sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.16.4 Best Regards, Wang
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Peder Worning ▴ 100
@peder-worning-3209
Last seen 10.2 years ago
Dear Jixin Wang, I use limma to normalize both one channel data normalizeBetweenArrays() and two channel data normalizeWithinArrays() I'll paste some code below to show what I do starting with the RG object. I am working with microRNA data and Exiqon arrays and you should find the parameters, that fit your experiment. You should also check, which channel is Cy3 and which is Cy5. My Cy3 is counter intuitively called RG$R. The Cy3.norm and Cy5.norm should be what you are asking for. I hope it can help you. Regards Peder rownames(RG) <- RG$genes[,6] #I use that to sum over spot replicates RGb = backgroundCorrect(RG, method="normexp", offset=50) cy3.channel = RGb$R cy3.channel.norm =normalizeBetweenArrays(log2(cy3.channel), method="quantile") #this is the Logscaled Cy3 data with four spots per probe cy5.channel = RGb$G cy5.channel.norm =normalizeBetweenArrays(log2(cy5.channel), method="quantile") #this is the Logscaled Cy5 data with four spots per probe MA = normalizeWithinArrays(RGb, method="loess", weights=RGb$weights) log.ratio <- MA$M # this is the Ratio data with four spots per probe #The median of the replicate probes: Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) Cy5.norm <- apply(cy5.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) LogRatio <- apply(logratio,2,function(v){tapply(v,names(v),function(x){median(x,na .r m=TRUE)})}) Best regards Exiqon A/S Peder Worning, Ph.D. Senior Scientist, Biomarker Discovery -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wang, Jixin Sent: Monday, March 09, 2009 6:58 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] RG.MA in limma Dear All, I have one question that has perplexed me for a while. I use two color arrays and I want to get the normalized log2 intensity values instead of M values in MA$M (say, I have four arrays and I want to get eight channels (red and green) of normalized expression data. How can I get them? I have checked the RG.MA function in R and have confused about this problem. I always got error messages whenever I try. Any help will be greatly appreciated! In R help for package limma, it said MA.RG converts an unlogged RGList object into an MAList object. MA.RG(object) is equivalent to normalizeWithinArrays(object,method="none"). RG.MA(object) converts back from an MAList object to a RGList object with unlogged intensities. > RG.MA$R <- 2^(MA$A + MA$M/2) Error in RG.MA$R <- 2^(MA$A + MA$M/2) : object of type 'closure' is not subsettable > RG.MA$G <- 2^(MA$A - MA$M/2) Error in RG.MA$G <- 2^(MA$A - MA$M/2) : object of type 'closure' is not subsettable sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.16.4 Best Regards, Wang _______________________________________________ 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
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Dear Peder, Many thanks for the kind help. Is the cy3.channel.norm and cy5.channel.norm I want according to your code? I got error when I ran your code. I don?t understand the Cy3.norm and Cy5.norm object even after I check the ?apply and ?tapply. Thanks. > Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),functi on(x){median(x,na.rm=TRUE)})}) Error in as.vector(x, mode) : invalid 'mode' argument > Cy5.norm <- apply(cy5.channel,2,function(v){tapply(v,names(v),functi on(x){median(x,na.rm=TRUE)})}) Error in as.vector(x, mode) : invalid 'mode' argument Here is the modified code following yours library(limma) setwd("C:/Documents and Settings/JWang/Desktop/la") targets <- readTargets("norm vs dev.txt") targets RG <- read.maimages(targets$FileName, source="genepix") RG RG = backgroundCorrect(RG, method="normexp", offset=50) cy3.channel = RG$G cy3.channel.norm =normalizeBetweenArrays(log2(cy3.channel), method="scale") cy5.channel = RG$R cy5.channel.norm =normalizeBetweenArrays(log2(cy5.channel), method="scale") MA = normalizeWithinArrays(RG, method="printtiploess") log.ratio <- MA$M write.csv(log.ratio,file="Mvalues.csv") write.table(cy3.channel.norm, file="cy3.channel.norm.txt") write.table(cy5.channel.norm, file="cy5.channel.norm.txt") Best Regards, Wang ----- Original Message ----- From: "Peder Worning" <pwo@exiqon.com> To: "Jixin Wang" <jixinwang at="" tamu.edu="">, bioconductor at stat.math.ethz.ch Sent: Monday, March 9, 2009 3:06:03 AM GMT -06:00 US/Canada Central Subject: RE: [BioC] RG.MA in limma Dear Jixin Wang, I use limma to normalize both one channel data normalizeBetweenArrays() and two channel data normalizeWithinArrays() I'll paste some code below to show what I do starting with the RG object. I am working with microRNA data and Exiqon arrays and you should find the parameters, that fit your experiment. You should also check, which channel is Cy3 and which is Cy5. My Cy3 is counter intuitively called RG$R. The Cy3.norm and Cy5.norm should be what you are asking for. I hope it can help you. Regards Peder rownames(RG) <- RG$genes[,6] #I use that to sum over spot replicates RGb = backgroundCorrect(RG, method="normexp", offset=50) cy3.channel = RGb$R cy3.channel.norm =normalizeBetweenArrays(log2(cy3.channel), method="quantile") #this is the Logscaled Cy3 data with four spots per probe cy5.channel = RGb$G cy5.channel.norm =normalizeBetweenArrays(log2(cy5.channel), method="quantile") #this is the Logscaled Cy5 data with four spots per probe MA = normalizeWithinArrays(RGb, method="loess", weights=RGb$weights) log.ratio <- MA$M # this is the Ratio data with four spots per probe #The median of the replicate probes: Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) Cy5.norm <- apply(cy5.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) LogRatio <- apply(logratio,2,function(v){tapply(v,names(v),function(x){median(x,na .r m=TRUE)})}) Best regards Exiqon A/S Peder Worning, Ph.D. Senior Scientist, Biomarker Discovery -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wang, Jixin Sent: Monday, March 09, 2009 6:58 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] RG.MA in limma Dear All, I have one question that has perplexed me for a while. I use two color arrays and I want to get the normalized log2 intensity values instead of M values in MA$M (say, I have four arrays and I want to get eight channels (red and green) of normalized expression data. How can I get them? I have checked the RG.MA function in R and have confused about this problem. I always got error messages whenever I try. Any help will be greatly appreciated! In R help for package limma, it said MA.RG converts an unlogged RGList object into an MAList object. MA.RG(object) is equivalent to normalizeWithinArrays(object,method="none"). RG.MA(object) converts back from an MAList object to a RGList object with unlogged intensities. > RG.MA$R <- 2^(MA$A + MA$M/2) Error in RG.MA$R <- 2^(MA$A + MA$M/2) : object of type 'closure' is not subsettable > RG.MA$G <- 2^(MA$A - MA$M/2) Error in RG.MA$G <- 2^(MA$A - MA$M/2) : object of type 'closure' is not subsettable sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.16.4 Best Regards, Wang _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dear Wang, The cy3.channel.norm and cy5.channel.norm are the normalized data you are looking for. The Cy3.norm and Cy5.norm are only relevant if each probe is spotted several times on the array and you then want to use the median (or mean) of these replicates. The apply function in my code sums over all spots with the same name (probeId), on our array every probe is spotted four times. There was two of missing line shifts in my mail, which may explain some of your troubles. Below is shown the code lines with the right line shift (if Outlook doesn't fool me again). I Hope it may help you Peder rownames(RG) <- RG$genes[,6] #I use that to sum over spot replicates RGb = backgroundCorrect(RG, method="normexp", offset=50) MA = normalizeWithinArrays(RGb, method="loess", weights=RGb$weights) log.ratio <- MA$M # this is the Ratio data with four spots per probe Best regards Exiqon A/S Peder Worning, Ph.D. -----Original Message----- From: Wang, Jixin [mailto:jixinwang@tamu.edu] Sent: Monday, March 09, 2009 7:38 PM To: Peder Worning Cc: Jixin Wang; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] RG.MA in limma Dear Peder, Many thanks for the kind help. Is the cy3.channel.norm and cy5.channel.norm I want according to your code? I got error when I ran your code. I don't understand the Cy3.norm and Cy5.norm object even after I check the ?apply and ?tapply. Thanks. > Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) Error in as.vector(x, mode) : invalid 'mode' argument > Cy5.norm <- apply(cy5.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) Error in as.vector(x, mode) : invalid 'mode' argument Here is the modified code following yours library(limma) setwd("C:/Documents and Settings/JWang/Desktop/la") targets <- readTargets("norm vs dev.txt") targets RG <- read.maimages(targets$FileName, source="genepix") RG RG = backgroundCorrect(RG, method="normexp", offset=50) cy3.channel = RG$G cy3.channel.norm =normalizeBetweenArrays(log2(cy3.channel), method="scale") cy5.channel = RG$R cy5.channel.norm =normalizeBetweenArrays(log2(cy5.channel), method="scale") MA = normalizeWithinArrays(RG, method="printtiploess") log.ratio <- MA$M write.csv(log.ratio,file="Mvalues.csv") write.table(cy3.channel.norm, file="cy3.channel.norm.txt") write.table(cy5.channel.norm, file="cy5.channel.norm.txt") Best Regards, Wang ----- Original Message ----- From: "Peder Worning" <pwo@exiqon.com> To: "Jixin Wang" <jixinwang at="" tamu.edu="">, bioconductor at stat.math.ethz.ch Sent: Monday, March 9, 2009 3:06:03 AM GMT -06:00 US/Canada Central Subject: RE: [BioC] RG.MA in limma Dear Jixin Wang, I use limma to normalize both one channel data normalizeBetweenArrays() and two channel data normalizeWithinArrays() I'll paste some code below to show what I do starting with the RG object. I am working with microRNA data and Exiqon arrays and you should find the parameters, that fit your experiment. You should also check, which channel is Cy3 and which is Cy5. My Cy3 is counter intuitively called RG$R. The Cy3.norm and Cy5.norm should be what you are asking for. I hope it can help you. Regards Peder rownames(RG) <- RG$genes[,6] #I use that to sum over spot replicates RGb = backgroundCorrect(RG, method="normexp", offset=50) cy3.channel = RGb$R cy3.channel.norm =normalizeBetweenArrays(log2(cy3.channel), method="quantile") #this is the Logscaled Cy3 data with four spots per probe cy5.channel = RGb$G cy5.channel.norm =normalizeBetweenArrays(log2(cy5.channel), method="quantile") #this is the Logscaled Cy5 data with four spots per probe MA = normalizeWithinArrays(RGb, method="loess", weights=RGb$weights) log.ratio <- MA$M # this is the Ratio data with four spots per probe #The median of the replicate probes: Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) Cy5.norm <- apply(cy5.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) LogRatio <- apply(logratio,2,function(v){tapply(v,names(v),function(x){median(x,na .r m=TRUE)})}) Best regards Exiqon A/S Peder Worning, Ph.D. Senior Scientist, Biomarker Discovery -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wang, Jixin Sent: Monday, March 09, 2009 6:58 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] RG.MA in limma Dear All, I have one question that has perplexed me for a while. I use two color arrays and I want to get the normalized log2 intensity values instead of M values in MA$M (say, I have four arrays and I want to get eight channels (red and green) of normalized expression data. How can I get them? I have checked the RG.MA function in R and have confused about this problem. I always got error messages whenever I try. Any help will be greatly appreciated! In R help for package limma, it said MA.RG converts an unlogged RGList object into an MAList object. MA.RG(object) is equivalent to normalizeWithinArrays(object,method="none"). RG.MA(object) converts back from an MAList object to a RGList object with unlogged intensities. > RG.MA$R <- 2^(MA$A + MA$M/2) Error in RG.MA$R <- 2^(MA$A + MA$M/2) : object of type 'closure' is not subsettable > RG.MA$G <- 2^(MA$A - MA$M/2) Error in RG.MA$G <- 2^(MA$A - MA$M/2) : object of type 'closure' is not subsettable sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.16.4 Best Regards, Wang _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Peder, Thanks a lot for the explanation. The code ran well now and the problem has been solved. Again, I appreciate your kind help! Best Regards, Wang ----- Original Message ----- From: "Peder Worning" <pwo@exiqon.com> To: "Jixin Wang" <jixinwang at="" tamu.edu=""> Cc: bioconductor at stat.math.ethz.ch Sent: Tuesday, March 10, 2009 2:41:48 AM GMT -06:00 US/Canada Central Subject: RE: [BioC] RG.MA in limma Dear Wang, The cy3.channel.norm and cy5.channel.norm are the normalized data you are looking for. The Cy3.norm and Cy5.norm are only relevant if each probe is spotted several times on the array and you then want to use the median (or mean) of these replicates. The apply function in my code sums over all spots with the same name (probeId), on our array every probe is spotted four times. There was two of missing line shifts in my mail, which may explain some of your troubles. Below is shown the code lines with the right line shift (if Outlook doesn't fool me again). I Hope it may help you Peder rownames(RG) <- RG$genes[,6] #I use that to sum over spot replicates RGb = backgroundCorrect(RG, method="normexp", offset=50) MA = normalizeWithinArrays(RGb, method="loess", weights=RGb$weights) log.ratio <- MA$M # this is the Ratio data with four spots per probe Best regards Exiqon A/S Peder Worning, Ph.D. -----Original Message----- From: Wang, Jixin [mailto:jixinwang@tamu.edu] Sent: Monday, March 09, 2009 7:38 PM To: Peder Worning Cc: Jixin Wang; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] RG.MA in limma Dear Peder, Many thanks for the kind help. Is the cy3.channel.norm and cy5.channel.norm I want according to your code? I got error when I ran your code. I don't understand the Cy3.norm and Cy5.norm object even after I check the ?apply and ?tapply. Thanks. > Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) Error in as.vector(x, mode) : invalid 'mode' argument > Cy5.norm <- apply(cy5.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) Error in as.vector(x, mode) : invalid 'mode' argument Here is the modified code following yours library(limma) setwd("C:/Documents and Settings/JWang/Desktop/la") targets <- readTargets("norm vs dev.txt") targets RG <- read.maimages(targets$FileName, source="genepix") RG RG = backgroundCorrect(RG, method="normexp", offset=50) cy3.channel = RG$G cy3.channel.norm =normalizeBetweenArrays(log2(cy3.channel), method="scale") cy5.channel = RG$R cy5.channel.norm =normalizeBetweenArrays(log2(cy5.channel), method="scale") MA = normalizeWithinArrays(RG, method="printtiploess") log.ratio <- MA$M write.csv(log.ratio,file="Mvalues.csv") write.table(cy3.channel.norm, file="cy3.channel.norm.txt") write.table(cy5.channel.norm, file="cy5.channel.norm.txt") Best Regards, Wang ----- Original Message ----- From: "Peder Worning" <pwo@exiqon.com> To: "Jixin Wang" <jixinwang at="" tamu.edu="">, bioconductor at stat.math.ethz.ch Sent: Monday, March 9, 2009 3:06:03 AM GMT -06:00 US/Canada Central Subject: RE: [BioC] RG.MA in limma Dear Jixin Wang, I use limma to normalize both one channel data normalizeBetweenArrays() and two channel data normalizeWithinArrays() I'll paste some code below to show what I do starting with the RG object. I am working with microRNA data and Exiqon arrays and you should find the parameters, that fit your experiment. You should also check, which channel is Cy3 and which is Cy5. My Cy3 is counter intuitively called RG$R. The Cy3.norm and Cy5.norm should be what you are asking for. I hope it can help you. Regards Peder rownames(RG) <- RG$genes[,6] #I use that to sum over spot replicates RGb = backgroundCorrect(RG, method="normexp", offset=50) cy3.channel = RGb$R cy3.channel.norm =normalizeBetweenArrays(log2(cy3.channel), method="quantile") #this is the Logscaled Cy3 data with four spots per probe cy5.channel = RGb$G cy5.channel.norm =normalizeBetweenArrays(log2(cy5.channel), method="quantile") #this is the Logscaled Cy5 data with four spots per probe MA = normalizeWithinArrays(RGb, method="loess", weights=RGb$weights) log.ratio <- MA$M # this is the Ratio data with four spots per probe #The median of the replicate probes: Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) Cy5.norm <- apply(cy5.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) LogRatio <- apply(logratio,2,function(v){tapply(v,names(v),function(x){median(x,na .r m=TRUE)})}) Best regards Exiqon A/S Peder Worning, Ph.D. Senior Scientist, Biomarker Discovery -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wang, Jixin Sent: Monday, March 09, 2009 6:58 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] RG.MA in limma Dear All, I have one question that has perplexed me for a while. I use two color arrays and I want to get the normalized log2 intensity values instead of M values in MA$M (say, I have four arrays and I want to get eight channels (red and green) of normalized expression data. How can I get them? I have checked the RG.MA function in R and have confused about this problem. I always got error messages whenever I try. Any help will be greatly appreciated! In R help for package limma, it said MA.RG converts an unlogged RGList object into an MAList object. MA.RG(object) is equivalent to normalizeWithinArrays(object,method="none"). RG.MA(object) converts back from an MAList object to a RGList object with unlogged intensities. > RG.MA$R <- 2^(MA$A + MA$M/2) Error in RG.MA$R <- 2^(MA$A + MA$M/2) : object of type 'closure' is not subsettable > RG.MA$G <- 2^(MA$A - MA$M/2) Error in RG.MA$G <- 2^(MA$A - MA$M/2) : object of type 'closure' is not subsettable sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.16.4 Best Regards, Wang _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Naomi Altman ★ 6.0k
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The problem is that you have tried to create a list called RG.MA without initializing it first. All you need to do is use the RG.MA function - i.e. RGnorm=RG.MA(MA) takes the M and A components of your normalized data "MA" and writes them back into an object called RGnorm along with any other components of MA, such as the annotation. --Naomi At 01:58 AM 3/9/2009, Wang, Jixin wrote: >Dear All, >I have one question that has perplexed me for a while. I use two >color arrays and I want to get the normalized log2 intensity values >instead of M values in MA$M (say, I have four arrays and I want to >get eight channels (red and green) of normalized expression data. >How can I get them? I have checked the RG.MA function in R and have >confused about this problem. I always got error messages whenever I >try. Any help will be greatly appreciated! > >In R help for package limma, it said >MA.RG converts an unlogged RGList object into an MAList object. >MA.RG(object) is equivalent to normalizeWithinArrays(object,method="none"). >RG.MA(object) converts back from an MAList object to a RGList object >with unlogged intensities. > > > RG.MA$R <- 2^(MA$A + MA$M/2) >Error in RG.MA$R <- 2^(MA$A + MA$M/2) : > object of type 'closure' is not subsettable > > RG.MA$G <- 2^(MA$A - MA$M/2) >Error in RG.MA$G <- 2^(MA$A - MA$M/2) : > object of type 'closure' is not subsettable > >sessionInfo() >R version 2.8.1 (2008-12-22) >i386-pc-mingw32 >locale: >LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >States.1252;LC_MONETARY=English_United >States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >attached base packages: >[1] stats graphics grDevices utils datasets methods base >other attached packages: >[1] limma_2.16.4 > >Best Regards, > >Wang > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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----- Original Message ----- From: "Naomi Altman" <naomi@stat.psu.edu> To: "Jixin Wang" <jixinwang at="" tamu.edu="">, bioconductor at stat.math.ethz.ch Sent: Monday, March 9, 2009 3:47:53 PM GMT -06:00 US/Canada Central Subject: Re: [BioC] RG.MA in limma The problem is that you have tried to create a list called RG.MA without initializing it first. All you need to do is use the RG.MA function - i.e. RGnorm=RG.MA(MA) takes the M and A components of your normalized data "MA" and writes them back into an object called RGnorm along with any other components of MA, such as the annotation. --Naomi At 01:58 AM 3/9/2009, Wang, Jixin wrote: >Dear All, >I have one question that has perplexed me for a while. I use two >color arrays and I want to get the normalized log2 intensity values >instead of M values in MA$M (say, I have four arrays and I want to >get eight channels (red and green) of normalized expression data. >How can I get them? I have checked the RG.MA function in R and have >confused about this problem. I always got error messages whenever I >try. Any help will be greatly appreciated! > >In R help for package limma, it said >MA.RG converts an unlogged RGList object into an MAList object. >MA.RG(object) is equivalent to normalizeWithinArrays(object,method="none"). >RG.MA(object) converts back from an MAList object to a RGList object >with unlogged intensities. > > > RG.MA$R <- 2^(MA$A + MA$M/2) >Error in RG.MA$R <- 2^(MA$A + MA$M/2) : > object of type 'closure' is not subsettable > > RG.MA$G <- 2^(MA$A - MA$M/2) >Error in RG.MA$G <- 2^(MA$A - MA$M/2) : > object of type 'closure' is not subsettable > >sessionInfo() >R version 2.8.1 (2008-12-22) >i386-pc-mingw32 >locale: >LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >States.1252;LC_MONETARY=English_United >States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >attached base packages: >[1] stats graphics grDevices utils datasets methods base >other attached packages: >[1] limma_2.16.4 > >Best Regards, > >Wang > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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Hi Naomi, Thanks for pointing out the problem and providing the hint. I appreciate your kind help! Best Regards, Wang ----- Original Message ----- From: "Naomi Altman" <naomi@stat.psu.edu> To: "Jixin Wang" <jixinwang at="" tamu.edu="">, bioconductor at stat.math.ethz.ch Sent: Monday, March 9, 2009 3:47:53 PM GMT -06:00 US/Canada Central Subject: Re: [BioC] RG.MA in limma The problem is that you have tried to create a list called RG.MA without initializing it first. All you need to do is use the RG.MA function - i.e. RGnorm=RG.MA(MA) takes the M and A components of your normalized data "MA" and writes them back into an object called RGnorm along with any other components of MA, such as the annotation. --Naomi At 01:58 AM 3/9/2009, Wang, Jixin wrote: >Dear All, >I have one question that has perplexed me for a while. I use two >color arrays and I want to get the normalized log2 intensity values >instead of M values in MA$M (say, I have four arrays and I want to >get eight channels (red and green) of normalized expression data. >How can I get them? I have checked the RG.MA function in R and have >confused about this problem. I always got error messages whenever I >try. Any help will be greatly appreciated! > >In R help for package limma, it said >MA.RG converts an unlogged RGList object into an MAList object. >MA.RG(object) is equivalent to normalizeWithinArrays(object,method="none"). >RG.MA(object) converts back from an MAList object to a RGList object >with unlogged intensities. > > > RG.MA$R <- 2^(MA$A + MA$M/2) >Error in RG.MA$R <- 2^(MA$A + MA$M/2) : > object of type 'closure' is not subsettable > > RG.MA$G <- 2^(MA$A - MA$M/2) >Error in RG.MA$G <- 2^(MA$A - MA$M/2) : > object of type 'closure' is not subsettable > >sessionInfo() >R version 2.8.1 (2008-12-22) >i386-pc-mingw32 >locale: >LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >States.1252;LC_MONETARY=English_United >States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >attached base packages: >[1] stats graphics grDevices utils datasets methods base >other attached packages: >[1] limma_2.16.4 > >Best Regards, > >Wang > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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