Cyclic Loess
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viritha kaza ▴ 580
@viritha-kaza-4318
Last seen 10.1 years ago
Hi, I am new to R statistics.I am doing microarray analysis. For which I have text file "__.txt[1]" which contains 47 columns and 43377 rows including the first row and first column with headers(names). I need to write a code to normalize using cyclic loess. I see this formula for it: normalize.loess(mat, subset = sample(1:(dim(mat)[1]), min(c(5000, nrow(mat)))), epsilon = 10^-2, maxit = 1, log.it = TRUE, verbose = TRUE, span = 2/3, family.loess = "symmetric") one of the paper said normalize.loess(data,epsilon=1,log.it=F,span=0.4,maxit=2). The data for epsilon,log.it,span and maxit have to be as mentioned in the paper.I am not aware as to what matrix parameters do I have to give. Any help on this will be appreciated. Thank u in advance [[alternative HTML version deleted]]
Microarray Microarray • 1.2k views
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viritha kaza ▴ 580
@viritha-kaza-4318
Last seen 10.1 years ago
Hi, Let me explain the issue clearly.I have taken the agilent 4x44 array series matrix file from geo and removed the above information except the expression data with ids in row 1 and column1 with GSMs.I am trying to normalise it with cyclic loess method. exprs <- as.matrix(read.table("GSE__.txt[1]", header = TRUE,sep = "\t", row.names = 1, as.is = TRUE)) then to normlize i used normalize.loess(exprs,epsilon=1,log.it=F,span=0.4,maxit=2) when I am doing this it doesnot show any error but my system shuts down.I guess this is because it is too much of processing.So is my method correct or should I have to break it and analyze if so how do I do it? I hope it is clear now. Thank you in advance, Viritha [[alternative HTML version deleted]]
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On 10/26/2010 08:10 AM, viritha kaza wrote: > Hi, > Let me explain the issue clearly.I have taken the agilent 4x44 array series > matrix file from geo and removed the above information except the expression > data with ids in row 1 and column1 with GSMs.I am trying to normalise it > with cyclic loess method. > > exprs <- as.matrix(read.table("GSE__.txt[1]", header = TRUE,sep = "\t", > row.names = 1, as.is = TRUE)) > > then to normlize i used > > normalize.loess(exprs,epsilon=1,log.it=F,span=0.4,maxit=2) > > when I am doing this it doesnot show any error but my system shuts down.I > guess this is because it is too much of processing.So is my method correct > or should I have to break it and analyze if so how do I do it? Hi Viritha -- it is unlikely a problem of too much data but rather version incompatibility in installed packages. Tell us sessionInfo() after following http://bioconductor.org/install/index.html#update-bioconductor- packages Since 'exprs' is just a matrix provide us with a reproducible example using random data, exprs = matrix(<...>) where <...> is sufficient to generate the problem on your system. Martin > > I hope it is clear now. > > Thank you in advance, > > Viritha > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Hi Morgan, The sessionInfo was R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.0 -Viritha On Tue, Oct 26, 2010 at 11:57 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 10/26/2010 08:10 AM, viritha kaza wrote: > > Hi, > > Let me explain the issue clearly.I have taken the agilent 4x44 array > series > > matrix file from geo and removed the above information except the > expression > > data with ids in row 1 and column1 with GSMs.I am trying to normalise it > > with cyclic loess method. > > > > exprs <- as.matrix(read.table("GSE__.txt[1]", header = TRUE,sep = "\t", > > row.names = 1, as.is = TRUE)) > > > > then to normlize i used > > > > normalize.loess(exprs,epsilon=1,log.it=F,span=0.4,maxit=2) > > > > when I am doing this it doesnot show any error but my system shuts down.I > > guess this is because it is too much of processing.So is my method > correct > > or should I have to break it and analyze if so how do I do it? > > Hi Viritha -- > > it is unlikely a problem of too much data but rather version > incompatibility in installed packages. Tell us > > sessionInfo() > > after following > > http://bioconductor.org/install/index.html#update-bioconductor- packages > > Since 'exprs' is just a matrix provide us with a reproducible example > using random data, exprs = matrix(<...>) where <...> is sufficient to > generate the problem on your system. > > Martin > > > > > I hope it is clear now. > > > > Thank you in advance, > > > > Viritha > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]]
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On 10/26/2010 09:45 AM, viritha kaza wrote: > > Hi Morgan, > The sessionInfo was > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > loaded via a namespace (and not attached): > [1] tools_2.10.0 you will want to update to the current released version of R, and to install the current version of the affy package source('http://bioconductor.org/biocLite.R') biocLite('affy') Provide sessionInfo() after attaching the affy package; I see something like > sessionInfo() R version 2.12.0 Patched (2010-10-17 r53355) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0 and provide a simple and reproducible example to illustrate the problem that you are having. For instance, I do not have a problem with > m = matrix(rnorm(100000 * 100), nrow=100000, ncol=100) > n = normalize.loess(m) Here exprs <- as.matrix(read.table("GSE__.txt[1]", header = TRUE,sep = "\t", row.names = 1, as.is = TRUE)) it might be that you do not have a numeric matrix or other oddity; confirm that it is as you expect. Martin > > -Viritha > > > > On Tue, Oct 26, 2010 at 11:57 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 10/26/2010 08:10 AM, viritha kaza wrote: > > Hi, > > Let me explain the issue clearly.I have taken the agilent 4x44 > array series > > matrix file from geo and removed the above information except the > expression > > data with ids in row 1 and column1 with GSMs.I am trying to > normalise it > > with cyclic loess method. > > > > exprs <- as.matrix(read.table("GSE__.txt[1]", header = TRUE,sep = > "\t", > > row.names = 1, as.is <http: as.is=""/> = TRUE)) > > > > then to normlize i used > > > > normalize.loess(exprs,epsilon=1,log.it > <http: log.it=""/>=F,span=0.4,maxit=2) > > > > when I am doing this it doesnot show any error but my system shuts > down.I > > guess this is because it is too much of processing.So is my method > correct > > or should I have to break it and analyze if so how do I do it? > > Hi Viritha -- > > it is unlikely a problem of too much data but rather version > incompatibility in installed packages. Tell us > > sessionInfo() > > after following > > http://bioconductor.org/install/index.html#update-bioconductor- packages > > Since 'exprs' is just a matrix provide us with a reproducible example > using random data, exprs = matrix(<...>) where <...> is sufficient to > generate the problem on your system. > > Martin > > > > > I hope it is clear now. > > > > Thank you in advance, > > > > Viritha > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch <mailto: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 > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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