limma how to ignoring background
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Guoneng Zhong ▴ 180
@guoneng-zhong-996
Last seen 9.7 years ago
Hi, My custom image result files do not have background readings. But limma's read.maimages ask me for it. How do I get around this? I tried lying to it by giving it some random numeric column in the result file, but am worried that when I do normalization or lmFit it will take that fake background into consideration. Any advice would be appreciated. Thanks, g -- Systems Programmer Yale Center for Medical Informatics fax: 203-737-5708
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@sean-davis-490
Last seen 4 months ago
United States
If RG is your RGList (from read.maimages), use: RG.no.background <- backgroundCorrect(RG,method='none') This will take out all background values so that they will not be used in further analysis. Sean On May 5, 2005, at 11:28 AM, Guoneng Zhong wrote: > > Hi, > > My custom image result files do not have background readings. But > limma's > read.maimages ask me for it. How do I get around this? I tried lying > to it by > giving it some random numeric column in the result file, but am > worried that > when I do normalization or lmFit it will take that fake background into > consideration. > > Any advice would be appreciated. > > Thanks, > g > > -- > > Systems Programmer > Yale Center for Medical Informatics > fax: 203-737-5708 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
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M PEREZ ▴ 110
@m-perez-1039
Last seen 9.7 years ago
Hi, I think that normalizeWithinArrays correct for background by default, so could be a good idea if you are going to do intrachip normalization add this MA <- normalizeWithinArrays(RG.no.background, bg.method="none") HTH Manuel Sean Davis <sdavis2@mail.nih.gov> escribió: If RG is your RGList (from read.maimages), use: RG.no.background <- backgroundCorrect(RG,method='none') This will take out all background values so that they will not be used in further analysis. Sean On May 5, 2005, at 11:28 AM, Guoneng Zhong wrote: > > Hi, > > My custom image result files do not have background readings. But > limma's > read.maimages ask me for it. How do I get around this? I tried lying > to it by > giving it some random numeric column in the result file, but am > worried that > when I do normalization or lmFit it will take that fake background into > consideration. > > Any advice would be appreciated. > > Thanks, > g > > -- > > Systems Programmer > Yale Center for Medical Informatics > fax: 203-737-5708 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor --------------------------------- [[alternative HTML version deleted]]
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So based on the two responses, should I have this: # note that the background is using the standard deviation columns just as place holder RG<-read.maimages(targets$FileName,columns=list(Rf="C5_Signal_Median", Rb="C5_Signal_SD",Gf="C3_Signal_Median",Gb="C3_Signal_SD"),annotation= c('Sel_Crt','Probe_Seq','Fea RG.no.background <- backgroundCorrect(RG,method='none') MA.lnorm <- normalizeWithinArrays(RG.no.background, method="loess",bg.method="none") Thanks, G -- Systems Programmer Yale Center for Medical Informatics fax: 203-737-5708 Quoting M PEREZ <perezperezmm@yahoo.es>: > Hi, > I think that normalizeWithinArrays correct for background > by default, so could be a good idea if you are going to do intrachip > normalization add this > MA <- normalizeWithinArrays(RG.no.background, bg.method="none") > > HTH > Manuel > > Sean Davis <sdavis2@mail.nih.gov> escribi?: > If RG is your RGList (from read.maimages), use: > > > RG.no.background <- backgroundCorrect(RG,method='none') > > This will take out all background values so that they will not be used > in further analysis. > > Sean > > On May 5, 2005, at 11:28 AM, Guoneng Zhong wrote: > > > > > Hi, > > > > My custom image result files do not have background readings. But > > limma's > > read.maimages ask me for it. How do I get around this? I tried lying > > to it by > > giving it some random numeric column in the result file, but am > > worried that > > when I do normalization or lmFit it will take that fake background into > > consideration. > > > > Any advice would be appreciated. > > > > Thanks, > > g > > > > -- > > > > Systems Programmer > > Yale Center for Medical Informatics > > fax: 203-737-5708 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > --------------------------------- > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >
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On May 5, 2005, at 1:12 PM, M PEREZ wrote: > Hi, > I think that normalizeWithinArrays correct for background > by default, so could be a good idea if you are going to do intrachip > normalization add this > MA <- normalizeWithinArrays(RG.no.background, bg.method="none") > It may be my version of limma, but I don't have a bg.method as an option for normalizeWithinArrays. In any case, RG.no.background contains no background information, so none will be used for normalization. Sean > Sean Davis <sdavis2@mail.nih.gov> escribio: > If RG is your RGList (from read.maimages), use: > > > RG.no.background <- backgroundCorrect(RG,method='none') > > This will take out all background values so that they will not be used > in further analysis. > > Sean > > On May 5, 2005, at 11:28 AM, Guoneng Zhong wrote: > >> >> Hi, >> >> My custom image result files do not have background readings. But >> limma's >> read.maimages ask me for it. How do I get around this? I tried lying >> to it by >> giving it some random numeric column in the result file, but am >> worried that >> when I do normalization or lmFit it will take that fake background >> into >> consideration. >> >> Any advice would be appreciated. >> >> Thanks, >> g >> >> -- >> >> Systems Programmer >> Yale Center for Medical Informatics >> fax: 203-737-5708 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > --------------------------------- > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
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M PEREZ ▴ 110
@m-perez-1039
Last seen 9.7 years ago
sorry is bc.method="none" , instead bg.method... I misspelled it Manuel Guoneng Zhong <guoneng.zhong@yale.edu> escribió: So based on the two responses, should I have this: # note that the background is using the standard deviation columns just as place holder RG<-read.maimages(targets$FileName,columns=list(Rf="C5_Signal_Median", Rb="C5_Signal_SD",Gf="C3_Signal_Median",Gb="C3_Signal_SD"),annotation= c('Sel_Crt','Probe_Seq','Fea RG.no.background <- backgroundCorrect(RG,method='none') MA.lnorm <- normalizeWithinArrays(RG.no.background, method="loess",bg.method="none") Thanks, G -- Systems Programmer Yale Center for Medical Informatics fax: 203-737-5708 Quoting M PEREZ : > Hi, > I think that normalizeWithinArrays correct for background > by default, so could be a good idea if you are going to do intrachip > normalization add this > MA <- normalizeWithinArrays(RG.no.background, bg.method="none") > > HTH > Manuel > > Sean Davis escribió: > If RG is your RGList (from read.maimages), use: > > > RG.no.background <- backgroundCorrect(RG,method='none') > > This will take out all background values so that they will not be used > in further analysis. > > Sean > > On May 5, 2005, at 11:28 AM, Guoneng Zhong wrote: > > > > > Hi, > > > > My custom image result files do not have background readings. But > > limma's > > read.maimages ask me for it. How do I get around this? I tried lying > > to it by > > giving it some random numeric column in the result file, but am > > worried that > > when I do normalization or lmFit it will take that fake background into > > consideration. > > > > Any advice would be appreciated. > > > > Thanks, > > g > > > > -- > > > > Systems Programmer > > Yale Center for Medical Informatics > > fax: 203-737-5708 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > --------------------------------- > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor --------------------------------- ĄComprueba las novedades! [[alternative HTML version deleted]]
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Having looked at the help files for normalizeWithinArrays and backgroundCorrect, I wonder if it is redundant to do both. I mean, if I do: RG.no.background <- backgroundCorrect(RG,method='none') Do I need to do?: MA <- normalizeWithinArrays(RG.no.background,method="loess",bc.method= "none") G -- Systems Programmer Yale Center for Medical Informatics fax: 203-737-5708 Quoting M PEREZ <perezperezmm@yahoo.es>: > sorry is bc.method="none" , instead bg.method... I misspelled it > > Manuel > > Guoneng Zhong <guoneng.zhong@yale.edu> escribi?: > So based on the two responses, should I have this: > > # note that the background is using the standard deviation columns just as > place > holder > RG<-read.maimages(targets$FileName,columns=list(Rf="C5_Signal_Median", Rb="C5_Signal_SD",Gf="C3_Signal_Median",Gb="C3_Signal_SD"),annotation= c('Sel_Crt','Probe_Seq','Fea > RG.no.background <- backgroundCorrect(RG,method='none') > MA.lnorm <- normalizeWithinArrays(RG.no.background, > method="loess",bg.method="none") > > Thanks, > G > > -- > > Systems Programmer > Yale Center for Medical Informatics > fax: 203-737-5708 > > > > Quoting M PEREZ > : > > > Hi, > > I think that normalizeWithinArrays correct for background > > by default, so could be a good idea if you are going to do intrachip > > normalization add this > > MA <- normalizeWithinArrays(RG.no.background, bg.method="none") > > > > HTH > > Manuel > > > > Sean Davis escribi?: > > If RG is your RGList (from read.maimages), use: > > > > > > RG.no.background <- backgroundCorrect(RG,method='none') > > > > This will take out all background values so that they will not be used > > in further analysis. > > > > Sean > > > > On May 5, 2005, at 11:28 AM, Guoneng Zhong wrote: > > > > > > > > Hi, > > > > > > My custom image result files do not have background readings. But > > > limma's > > > read.maimages ask me for it. How do I get around this? I tried lying > > > to it by > > > giving it some random numeric column in the result file, but am > > > worried that > > > when I do normalization or lmFit it will take that fake background into > > > consideration. > > > > > > Any advice would be appreciated. > > > > > > Thanks, > > > g > > > > > > -- > > > > > > Systems Programmer > > > Yale Center for Medical Informatics > > > fax: 203-737-5708 > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > --------------------------------- > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > --------------------------------- > > > ?Comprueba las novedades! > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >
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yeah, I think you are righ, you can choose between two options. if you use MA <- normalizeWithinArrays(RG, method="loess", bc.method="none") you can save just a little bit of code.. Manuel Guoneng Zhong <guoneng.zhong@yale.edu> escribió: Having looked at the help files for normalizeWithinArrays and backgroundCorrect, I wonder if it is redundant to do both. I mean, if I do: RG.no.background <- backgroundCorrect(RG,method='none') Do I need to do?: MA <- normalizeWithinArrays(RG.no.background,method="loess",bc.method= "none") G -- Systems Programmer Yale Center for Medical Informatics fax: 203-737-5708 Quoting M PEREZ : > sorry is bc.method="none" , instead bg.method... I misspelled it > > Manuel > > Guoneng Zhong escribió: > So based on the two responses, should I have this: > > # note that the background is using the standard deviation columns just as > place > holder > RG<-read.maimages(targets$FileName,columns=list(Rf="C5_Signal_Median", Rb="C5_Signal_SD",Gf="C3_Signal_Median",Gb="C3_Signal_SD"),annotation= c('Sel_Crt','Probe_Seq','Fea > RG.no.background <- backgroundCorrect(RG,method='none') > MA.lnorm <- normalizeWithinArrays(RG.no.background, > method="loess",bg.method="none") > > Thanks, > G > > -- > > Systems Programmer > Yale Center for Medical Informatics > fax: 203-737-5708 > > > > Quoting M PEREZ > : > > > Hi, > > I think that normalizeWithinArrays correct for background > > by default, so could be a good idea if you are going to do intrachip > > normalization add this > > MA <- normalizeWithinArrays(RG.no.background, bg.method="none") > > > > HTH > > Manuel > > > > Sean Davis escribió: > > If RG is your RGList (from read.maimages), use: > > > > > > RG.no.background <- backgroundCorrect(RG,method='none') > > > > This will take out all background values so that they will not be used > > in further analysis. > > > > Sean > > > > On May 5, 2005, at 11:28 AM, Guoneng Zhong wrote: > > > > > > > > Hi, > > > > > > My custom image result files do not have background readings. But > > > limma's > > > read.maimages ask me for it. How do I get around this? I tried lying > > > to it by > > > giving it some random numeric column in the result file, but am > > > worried that > > > when I do normalization or lmFit it will take that fake background into > > > consideration. > > > > > > Any advice would be appreciated. > > > > > > Thanks, > > > g > > > > > > -- > > > > > > Systems Programmer > > > Yale Center for Medical Informatics > > > fax: 203-737-5708 > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > --------------------------------- > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > --------------------------------- > > > ĄComprueba las novedades! > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor --------------------------------- ĄComprueba las novedades! [[alternative HTML version deleted]]
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