boxplot of MM data and normalization
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 8.8 years ago
Hi list, My first question is a follow-up of an old post ( https://stat.ethz.ch/pipermail/bioconductor/2003-October/002660.html ). I don't think boxplot(myDat, with="MM") works. Please see below. I'm using R 2.3.0, WinXP, affy 1.10.0. My second question is: do differenet normalization options in 'expresso' do anything to the MM probes? thanks, ...Tao > data(affybatch.example) > par(mfrow=c(1,2)) > boxplot(affybatch.example, with="PM") > boxplot(affybatch.example, with="MM") > > boxplot(affybatch.example, with="PM")$stat [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > boxplot(affybatch.example, with="MM")$stat [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > > > boxplot(data.frame(log2(pm(affybatch.example))))$stat [,1] [,2] [,3] [1,] 6.175924 5.700440 5.942515 [2,] 6.768184 6.345183 6.549205 [3,] 7.108524 6.791814 6.882643 [4,] 8.012624 7.660353 7.749199 [5,] 9.878051 9.612868 9.541097 > boxplot(data.frame(log2(mm(affybatch.example))))$stat [,1] [,2] [,3] [1,] 6.205549 5.672425 5.995485 [2,] 6.820179 6.397461 6.589464 [3,] 7.285402 6.965784 7.056908 [4,] 8.657851 8.224002 8.359309 [5,] 11.398904 10.959278 10.990104 >
Normalization affy Normalization affy • 1.1k views
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 8.8 years ago
Hi Jim, Thanks for the quick reply! With the lower case letters, I don't think it's working either. See below. Regarding my second question, I would assume 'expresso' uses the default parameters, which should be 'separate' for 'type' in most cases, for the normalization method it specified when no 'normalize.param' are supplied? best, ...Tao > data(affybatch.example) > par(mfrow=c(1,2)) > boxplot(affybatch.example, with="pm")$stat [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > boxplot(affybatch.example, with="mm")$stat [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 ----- Original Message - From: James W. MacDonald <jmacdon@med.umich.edu> To: "Shi, Tao" <shidaxia at="" yahoo.com=""> Cc: bioconductor at stat.math.ethz.ch Sent: Tuesday, October 3, 2006 12:35:21 PM Subject: Re: [BioC] boxplot of MM data and normalization Shi, Tao wrote: > Hi list, > > My first question is a follow-up of an old post ( > https://stat.ethz.ch/pipermail/bioconductor/2003-October/002660.html > ). I don't think boxplot(myDat, with="MM") works. Please see below. > I'm using R 2.3.0, WinXP, affy 1.10.0. You are correct; with = "MM" doesn't work because R is case sensitive, and the correct argument is "mm". > > My second question is: do differenet normalization options in > 'expresso' do anything to the MM probes? Well, a quick look at ?normalize.loess gives this: Details: The type arguement should be one of '"separate","pmonly","mmonly","together"' which indicates whether to normalize only one probe type (PM,MM) or both together or separately. Looking at the help pages for the other methods may be just as helpful ;-P Best, Jim > > thanks, > > ...Tao > > > >> data(affybatch.example) par(mfrow=c(1,2)) >> boxplot(affybatch.example, with="PM") boxplot(affybatch.example, >> with="MM") >> >> boxplot(affybatch.example, with="PM")$stat > > [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] > 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] > 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > >> boxplot(affybatch.example, with="MM")$stat > > [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] > 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] > 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > >> >> boxplot(data.frame(log2(pm(affybatch.example))))$stat > > [,1] [,2] [,3] [1,] 6.175924 5.700440 5.942515 [2,] 6.768184 > 6.345183 6.549205 [3,] 7.108524 6.791814 6.882643 [4,] 8.012624 > 7.660353 7.749199 [5,] 9.878051 9.612868 9.541097 > >> boxplot(data.frame(log2(mm(affybatch.example))))$stat > > [,1] [,2] [,3] [1,] 6.205549 5.672425 5.995485 [2,] > 6.820179 6.397461 6.589464 [3,] 7.285402 6.965784 7.056908 [4,] > 8.657851 8.224002 8.359309 [5,] 11.398904 10.959278 10.990104 > > > _______________________________________________ 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Sorry; which = "pm", not with. Jim Shi, Tao wrote: > Hi Jim, > > Thanks for the quick reply! > > With the lower case letters, I don't think it's working either. See > below. > > Regarding my second question, I would assume 'expresso' uses the > default parameters, which should be 'separate' for 'type' in most > cases, for the normalization method it specified when no > 'normalize.param' are supplied? > > best, ...Tao > > > >> data(affybatch.example) par(mfrow=c(1,2)) >> boxplot(affybatch.example, with="pm")$stat > > [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] > 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] > 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > >> boxplot(affybatch.example, with="mm")$stat > > [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] > 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] > 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > > > > > > ----- Original Message - From: James W. MacDonald > <jmacdon at="" med.umich.edu=""> To: "Shi, Tao" <shidaxia at="" yahoo.com=""> Cc: > bioconductor at stat.math.ethz.ch Sent: Tuesday, October 3, 2006 > 12:35:21 PM Subject: Re: [BioC] boxplot of MM data and normalization > > Shi, Tao wrote: > > >> Hi list, > > > >> My first question is a follow-up of an old post ( > > >> https://stat.ethz.ch/pipermail/bioconductor/2003-October/002660.html >> > > >> ). I don't think boxplot(myDat, with="MM") works. Please see >> below. > > >> I'm using R 2.3.0, WinXP, affy 1.10.0. > > > > > You are correct; with = "MM" doesn't work because R is case > sensitive, > > and the correct argument is "mm". > > > > > >> My second question is: do differenet normalization options in > > >> 'expresso' do anything to the MM probes? > > > > > Well, a quick look at ?normalize.loess gives this: > > > > Details: > > > > The type arguement should be one of > > '"separate","pmonly","mmonly","together"' which indicates whether > > to normalize only one probe type (PM,MM) or both together or > > separately. > > > > Looking at the help pages for the other methods may be just as > helpful ;-P > > > > Best, > > > > Jim > > > > > > > >> thanks, > > > >> ...Tao > > > > > >>> data(affybatch.example) par(mfrow=c(1,2)) > > >>> boxplot(affybatch.example, with="PM") boxplot(affybatch.example, > > >>> with="MM") > > > >>> boxplot(affybatch.example, with="PM")$stat > > > >> [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] > > >> 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 >> [4,] > > >> 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > > > >>> boxplot(affybatch.example, with="MM")$stat > > > >> [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] > > >> 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 >> [4,] > > >> 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > > > > >>> boxplot(data.frame(log2(pm(affybatch.example))))$stat > > > >> [,1] [,2] [,3] [1,] 6.175924 5.700440 5.942515 [2,] >> 6.768184 > > >> 6.345183 6.549205 [3,] 7.108524 6.791814 6.882643 [4,] 8.012624 > > >> 7.660353 7.749199 [5,] 9.878051 9.612868 9.541097 > > > >>> boxplot(data.frame(log2(mm(affybatch.example))))$stat > > > >> [,1] [,2] [,3] [1,] 6.205549 5.672425 5.995485 [2,] > > >> 6.820179 6.397461 6.589464 [3,] 7.285402 6.965784 7.056908 >> [4,] > > >> 8.657851 8.224002 8.359309 [5,] 11.398904 10.959278 10.990104 > > > > >> _______________________________________________ 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 > > > > > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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@james-w-macdonald-5106
Last seen 19 minutes ago
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Shi, Tao wrote: > Hi list, > > My first question is a follow-up of an old post ( > https://stat.ethz.ch/pipermail/bioconductor/2003-October/002660.html > ). I don't think boxplot(myDat, with="MM") works. Please see below. > I'm using R 2.3.0, WinXP, affy 1.10.0. You are correct; with = "MM" doesn't work because R is case sensitive, and the correct argument is "mm". > > My second question is: do differenet normalization options in > 'expresso' do anything to the MM probes? Well, a quick look at ?normalize.loess gives this: Details: The type arguement should be one of '"separate","pmonly","mmonly","together"' which indicates whether to normalize only one probe type (PM,MM) or both together or separately. Looking at the help pages for the other methods may be just as helpful ;-P Best, Jim > > thanks, > > ...Tao > > > >> data(affybatch.example) par(mfrow=c(1,2)) >> boxplot(affybatch.example, with="PM") boxplot(affybatch.example, >> with="MM") >> >> boxplot(affybatch.example, with="PM")$stat > > [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] > 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] > 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > >> boxplot(affybatch.example, with="MM")$stat > > [,1] [,2] [,3] [1,] 6.175924 5.672425 5.942515 [2,] > 6.794416 6.375039 6.574404 [3,] 7.179909 6.870365 6.954196 [4,] > 8.321921 7.927185 8.053383 [5,] 14.176664 13.515946 14.188434 > >> >> boxplot(data.frame(log2(pm(affybatch.example))))$stat > > [,1] [,2] [,3] [1,] 6.175924 5.700440 5.942515 [2,] 6.768184 > 6.345183 6.549205 [3,] 7.108524 6.791814 6.882643 [4,] 8.012624 > 7.660353 7.749199 [5,] 9.878051 9.612868 9.541097 > >> boxplot(data.frame(log2(mm(affybatch.example))))$stat > > [,1] [,2] [,3] [1,] 6.205549 5.672425 5.995485 [2,] > 6.820179 6.397461 6.589464 [3,] 7.285402 6.965784 7.056908 [4,] > 8.657851 8.224002 8.359309 [5,] 11.398904 10.959278 10.990104 > > > _______________________________________________ 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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