normalize.invariantset
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@lgautieralternorg-747
Last seen 10.3 years ago
> > Hello, > The Gentleman book suggests to do variant normalizations one should do > 'normalize(object, method="<some method="">"). We would like to know if one > selects "invariantset", what does the code use for default settings? The > R > code for normalize.AffyBatch.invariantset doesn't show a default set, What do you mean by "default set" ? What you write below suggests that the issue is about "default parameters". > and > it seems to indicate that one should specify a baseline type from median, > mean, pseudo-median, and pseudo-mean, This is what the code says. > and a type from separate, pmonly, > mmonly, or together. This relates to the type of methods for dealing with Perfect Match (PM) and Mismatch (MM) probes. (Which is convenient, is nicely unified accross normalization methods in affy, and was added by Ben Bolstad if I remember it correctly... and I suspect he added the baseline type as well). > So what does 'normalize(object,method="invariantset") actually do? Did you already check either the help page for the function 'normalize.AffyBatch.invariantset', or a manual on how R is dealing with default parameters in the signature of a function ? Hoping this helps, Laurent > Dan > >
Normalization Normalization • 1.0k views
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Daniel Pick ▴ 50
@daniel-pick-1467
Last seen 10.3 years ago
Hello, The Gentleman book suggests to do variant normalizations one should do 'normalize(object, method="<some method="">"). We would like to know if one selects "invariantset", what does the code use for default settings? The R code for normalize.AffyBatch.invariantset doesn't show a default set, and it seems to indicate that one should specify a baseline type from median, mean, pseudo-median, and pseudo-mean, and a type from separate, pmonly, mmonly, or together. So what does 'normalize(object,method="invariantset") actually do? Dan
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Daniel Pick wrote: > Hello, > The Gentleman book suggests to do variant normalizations one should do > 'normalize(object, method="<some method="">"). We would like to know if one > selects "invariantset", what does the code use for default settings? The R > code for normalize.AffyBatch.invariantset doesn't show a default set, and > it seems to indicate that one should specify a baseline type from median, > mean, pseudo-median, and pseudo-mean, and a type from separate, pmonly, > mmonly, or together. > So what does 'normalize(object,method="invariantset") actually do? It uses the first option for all arguments that have a character vector of choices. For instance, the code says function (abatch, prd.td = c(0.003, 0.007), verbose = FALSE, baseline.type = c("mean", "median", "pseudo-mean", "pseudo- median"), type = c("separate", "pmonly", "mmonly", "together")) so normalize(object, method="invariantset") will call normalize.AffyBatch.invariantset(object, prd.td = c(0.003, 0.007), verbose = FALSE, baseline.type = "mean", type = "separate") You have to supply an argument for baseline.type and type if you want something different. HTH, Jim > > Dan > > _______________________________________________ > 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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Hi, Thank you very much for this informative reply. Are you sure about this behavior? I have queried the code contributor about this, and he didn't express this definitely. The latest R Language definition (version 2.2.0, dated Oct 6, 2005) does not say that the first choice in an argument list is used by default. In fact, it says that a default is specified by setting 'symbol = default' construct, as was done with 'verbose = FALSE' That led me to question the actual behavior of the call. If you look at the R code for normalize.AffyBatch.invariantset, you will see that there are a bunch of 'if' clauses for each baseline type, but none of them is set as the default. So I am really wondering about the performance of the call. It's not at all clear to me that the code behaves as you suggest. Dan "James W. MacDonald" <jmacdon at="" med.umic="" to="" h.edu=""> Daniel Pick <daniel.pick at="" biogenidec.com=""> 24-Mar-2006 10:51 cc AM bioconductor at stat.math.ethz.ch Subject Message Size: 5.0 Re: [BioC] normalize.invariantset KB Daniel Pick wrote: > Hello, > The Gentleman book suggests to do variant normalizations one should do > 'normalize(object, method="<some method="">"). We would like to know if one > selects "invariantset", what does the code use for default settings? The R > code for normalize.AffyBatch.invariantset doesn't show a default set, and > it seems to indicate that one should specify a baseline type from median, > mean, pseudo-median, and pseudo-mean, and a type from separate, pmonly, > mmonly, or together. > So what does 'normalize(object,method="invariantset") actually do? It uses the first option for all arguments that have a character vector of choices. For instance, the code says function (abatch, prd.td = c(0.003, 0.007), verbose = FALSE, baseline.type = c("mean", "median", "pseudo-mean", "pseudo- median"), type = c("separate", "pmonly", "mmonly", "together")) so normalize(object, method="invariantset") will call normalize.AffyBatch.invariantset(object, prd.td = c(0.003, 0.007), verbose = FALSE, baseline.type = "mean", type = "separate") You have to supply an argument for baseline.type and type if you want something different. HTH, Jim > > Dan > > _______________________________________________ > 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 1 hour ago
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Daniel Pick wrote: > Hi, > Thank you very much for this informative reply. > Are you sure about this behavior? I have queried the code contributor > about this, and he didn't express this definitely. The latest R Language > definition (version 2.2.0, dated Oct 6, 2005) does not say that the first > choice in an argument list is used by default. In fact, it says that a > default is specified by setting 'symbol = default' construct, as was done > with 'verbose = FALSE' That led me to question the actual behavior of the > call. > If you look at the R code for normalize.AffyBatch.invariantset, you > will see that there are a bunch of 'if' clauses for each baseline type, but > none of them is set as the default. So I am really wondering about the > performance of the call. It's not at all clear to me that the code behaves > as you suggest. You are not looking at the code for the function normalize.AffyBatch.invariantset(). You are looking at a function that is defined within that function called (of all things) do.normalize.AffyBatch.invariantset(). At the end of this function you will see two lines: type <- match.arg(type) baseline.type <- match.arg(baseline.type) What match.arg() does is to match the argument supplied with a vector of choices. From the help for match.arg(): Details: In the one-argument form 'match.arg(arg)', the choices are obtained from a default setting for the formal argument 'arg' of the function from which 'match.arg' was called. So if you don't specify an argument for type and baseline.type, the default will be the first value in the character vector for each argument. As further proof: > library(affy) > data(affybatch.example) > debug(normalize.AffyBatch.invariantset) > normalize(affybatch.example, method="invariantset") debugging in: normalize.AffyBatch.invariantset(object, ...) debug: { do.normalize.Affybatch.invariantset <- function(abatch, pms, prd.td, baseline.type) { [Snip] Browse[1]> debug: type <- match.arg(type) Browse[1]> debug: baseline.type <- match.arg(baseline.type) Browse[1]> [Snip] Browse[1]> type [1] "separate" Browse[1]> baseline.type [1] "mean" HTH, Jim > > Dan > > > > "James W. > MacDonald" > <jmacdon at="" med.umic="" to=""> h.edu> Daniel Pick > <daniel.pick at="" biogenidec.com=""> > 24-Mar-2006 10:51 cc > AM bioconductor at stat.math.ethz.ch > Subject > Message Size: 5.0 Re: [BioC] normalize.invariantset > KB > > > > > > > > > > Daniel Pick wrote: > >>Hello, >> The Gentleman book suggests to do variant normalizations one should > > do > >>'normalize(object, method="<some method="">"). We would like to know if one >>selects "invariantset", what does the code use for default settings? The > > R > >>code for normalize.AffyBatch.invariantset doesn't show a default set, and >>it seems to indicate that one should specify a baseline type from median, >>mean, pseudo-median, and pseudo-mean, and a type from separate, pmonly, >>mmonly, or together. >>So what does 'normalize(object,method="invariantset") actually do? > > > It uses the first option for all arguments that have a character vector > of choices. For instance, the code says > > function (abatch, prd.td = c(0.003, 0.007), verbose = FALSE, > baseline.type = c("mean", "median", "pseudo-mean", "pseudo- median"), > type = c("separate", "pmonly", "mmonly", "together")) > > so normalize(object, method="invariantset") will call > normalize.AffyBatch.invariantset(object, prd.td = c(0.003, 0.007), > verbose = FALSE, baseline.type = "mean", type = "separate") > > You have to supply an argument for baseline.type and type if you want > something different. > > HTH, > > Jim > > > >>Dan >> >>_______________________________________________ >>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. > > -- 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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Naomi Altman ★ 6.0k
@naomi-altman-380
Last seen 3.7 years ago
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When in doubt, copy the function to a new function, edit, and add some print statements. Then you can see what the routine is actually using. One of the great things about R is that you can see and modify the code. --Naomi At 02:45 PM 3/24/2006, Daniel Pick wrote: >Hi, > Thank you very much for this informative reply. > Are you sure about this behavior? I have queried the code contributor >about this, and he didn't express this definitely. The latest R Language >definition (version 2.2.0, dated Oct 6, 2005) does not say that the first >choice in an argument list is used by default. In fact, it says that a >default is specified by setting 'symbol = default' construct, as was done >with 'verbose = FALSE' That led me to question the actual behavior of the >call. > If you look at the R code for normalize.AffyBatch.invariantset, you >will see that there are a bunch of 'if' clauses for each baseline type, but >none of them is set as the default. So I am really wondering about the >performance of the call. It's not at all clear to me that the code behaves >as you suggest. > >Dan > > > > "James W. > MacDonald" > <jmacdon at="" med.umic="" to=""> h.edu> Daniel Pick > <daniel.pick at="" biogenidec.com=""> > 24-Mar-2006 10:51 cc > AM bioconductor at stat.math.ethz.ch > Subject > Message Size: 5.0 Re: [BioC] normalize.invariantset > KB > > > > > > > > > >Daniel Pick wrote: > > Hello, > > The Gentleman book suggests to do variant normalizations one should >do > > 'normalize(object, method="<some method="">"). We would like to know if one > > selects "invariantset", what does the code use for default settings? The >R > > code for normalize.AffyBatch.invariantset doesn't show a default set, and > > it seems to indicate that one should specify a baseline type from median, > > mean, pseudo-median, and pseudo-mean, and a type from separate, pmonly, > > mmonly, or together. > > So what does 'normalize(object,method="invariantset") actually do? > >It uses the first option for all arguments that have a character vector >of choices. For instance, the code says > >function (abatch, prd.td = c(0.003, 0.007), verbose = FALSE, > baseline.type = c("mean", "median", "pseudo-mean", "pseudo- median"), > type = c("separate", "pmonly", "mmonly", "together")) > >so normalize(object, method="invariantset") will call >normalize.AffyBatch.invariantset(object, prd.td = c(0.003, 0.007), >verbose = FALSE, baseline.type = "mean", type = "separate") > >You have to supply an argument for baseline.type and type if you want >something different. > >HTH, > >Jim > > > > > > Dan > > > > _______________________________________________ > > 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. > >_______________________________________________ >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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