exonmap RMA function
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@martin-morgan-1513
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"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Hi Yuan, > > Jay an wrote: >> Hello, >> I got several .CEL files to do RMA using exonmap library below: >> > raw.data <- read.exon() >>> raw.data at cdfName <- "exon.pmcdf" >>> x.rma <- rma(raw.data) >>> write.table(x.rma, file="x.csv", sep="\t") > > I'm surprised that worked. If you want to write out the expression There's a method that converts an ExpressionSet into a data.frame, taking the transpose of the expression values and cbind'ing (adding as columns) the phenotypic data. > library(Biobase) > data(sample.ExpressionSet) > names(as(sample.ExpressionSet, "data.frame")) [1] "AFFX.MurIL2_at" "AFFX.MurIL10_at" [3] "AFFX.MurIL4_at" "AFFX.MurFAS_at" [5] "AFFX.BioB.5_at" "AFFX.BioB.M_at" ... [499] "X31738_at" "X31739_at" [501] "sex" "type" [503] "score" This gets invoked by write.table and other functions that try to coerce their arguments to a data.frame. This can be convenient for instance in machine learning, where you can write a formula with '.' to indicate 'all columns' of a data.frame, and just provide the (probably filtered) ExpressionSet as the data argument. The affyPLM package might help to 'get RMA expression levels for each probe'. Martin > values you want to use write.exprs(), not write.table(), which is > intended to write out data.frames or matrices (and x.rma is neither). > > Best, > > Jim > > >> the file x.csv has 1,411,190 conlumns titles "x231501" "X2315102".... >> can you please tell me what the meaning of columns? are they >> expression levels for all probesets? >> how can i get RMA expression level for each probe? >> >> >> thanks >> Yuan >> >> >> >> >> --------------------------------- >> >> [[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 > > -- > 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 > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
Microarray Cancer affyPLM exonmap Microarray Cancer affyPLM exonmap • 781 views
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Jay an ▴ 60
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On Jan 17, 2008, at 4:57 PM, Jay an wrote: > Thanks Martin and James, > > after doing write.table(x.rma, file="x.csv", sep="\t") > the file x.csv has 1,411,190 conlumns titles "x231501" "X2315102".... > can you please tell me what the meaning of columns? are they > expression levels for all probesets? > how can i get RMA expression level for each probe? What do you mean by this. Typically summarization is considered part of the RMA method and after summarization you have probeset level values, not probe level values. Kasper > > Yuan > > > Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > "James W. MacDonald" writes: > >> Hi Yuan, >> >> Jay an wrote: >>> Hello, >>> I got several .CEL files to do RMA using exonmap library below: >>>> raw.data <- read.exon() >>>> raw.data at cdfName <- "exon.pmcdf" >>>> x.rma <- rma(raw.data) >>>> write.table(x.rma, file="x.csv", sep="\t") >> >> I'm surprised that worked. If you want to write out the expression > > There's a method that converts an ExpressionSet into a data.frame, > taking the transpose of the expression values and cbind'ing (adding as > columns) the phenotypic data. > >> library(Biobase) >> data(sample.ExpressionSet) >> names(as(sample.ExpressionSet, "data.frame")) > [1] "AFFX.MurIL2_at" "AFFX.MurIL10_at" > [3] "AFFX.MurIL4_at" "AFFX.MurFAS_at" > [5] "AFFX.BioB.5_at" "AFFX.BioB.M_at" > ... > [499] "X31738_at" "X31739_at" > [501] "sex" "type" > [503] "score" > > This gets invoked by write.table and other functions that try to > coerce their arguments to a data.frame. This can be convenient for > instance in machine learning, where you can write a formula with '.' > to indicate 'all columns' of a data.frame, and just provide the > (probably filtered) ExpressionSet as the data argument. > > The affyPLM package might help to 'get RMA expression levels for each > probe'. > > Martin > >> values you want to use write.exprs(), not write.table(), which is >> intended to write out data.frames or matrices (and x.rma is neither). >> >> Best, >> >> Jim >> >> >>> the file x.csv has 1,411,190 conlumns titles "x231501" >>> "X2315102".... >>> can you please tell me what the meaning of columns? are they >>> expression levels for all probesets? >>> how can i get RMA expression level for each probe? >>> >>> >>> thanks >>> Yuan >>> >>> >>> >>> >>> --------------------------------- >>> >>> [[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 >> >> -- >> 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 >> >> _______________________________________________ >> 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 > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M2 B169 > Phone: (206) 667-2793 > > > > --------------------------------- > > > --------------------------------- > > [[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
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@martin-morgan-1513
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Jay an <jayuan2007 at="" yahoo.com=""> writes: > the whole R source code shoud be: > >raw.data <- read.exon() >> raw.data at cdfName <- "exon.pmcdf" >> x.rma <- rma(raw.data) >> write.table(x.rma, file="x.csv", sep="\t") > > the generated file x.csv has 1,411,190 conlumns titles "x231501" "X2315102".... > can you please answer the following questions? > 1. how to find relation bewteen probset and probes in exonmap library? These are in the exon.pmcdf environment, e.g,. > library(exonmap) > library(exon.pmcdf) > data(exonmap) > mget(featureNames(x.rma), exon.pmcdf) library(exon.pmcdf) attaches the exon.pmcdf environment to the search path. data(exonmap) loads the sample data set 'x.rma' from the exonmap package. data(exonmap) is included here to provide an example that all on the list can reproduce; do not perform this step if you have your own data. x.rma is of class 'ExpressionSet', and is a subset of the result of applying rma to six CEL files as described on its help page (?x.rma). featureNames extracts the names of the 'features' (probe names) of the ExpressionSet, as described on the ExpressionSet help page (?ExpressionSet). mget looks up each feature name in the exon.pmcdf environment. The return value of mget is a named list (as described in the mget help page, ?mget), with each element in the list corresponding to an element in featureName, and containing the probes mapping to that featureName. This assumes that you have downloaded and installed the exon.pmcdf library, following the instructions in the exonmap package. > 2. is it possible to find normalized value for each probe value ? Follow Kasper's suggestion and review your understanding of the rma function (see the rma help page, ?rma for references): the rma function performs background correction, normalization, and summarization of probes into probe sets, so it does not make sense to ask for probe-level values from rma. Perhaps you would like to perform background correction and / or normalization without summary. See the help page ?bg.correct or ?normalize in the 'affy' package, or the affyPLM package for more advanced use. >> can you please tell me what the meaning of columns? are they >> expression levels for all probesets? Each column is a different probe set. Each row is a different sample. Each probe set name is prefixed with an 'X'. This is a consequence of using write.table. For an ExpressionSet, write.table also appends columns of phenotypic data, so several columns at the end of the table may not be probe sets. As mentioned by James, write.exprs is usually more appropriate. write.exprs saves the expression values with rows as probe sets and columns as samples. In this case, row names (i.e., probe sets) are not prefixed with 'x'. One would normally only use these functions to export the data for use in other programs. Methods described on the 'ExpressionSet' help page (?ExpressionSet) would be used in an interactive session or R script. Martin >> how can i get RMA expression level for each probe? > > > Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> wrote: > > On Jan 17, 2008, at 4:57 PM, Jay an wrote: > >> Thanks Martin and James, >> >> after doing write.table(x.rma, file="x.csv", sep="\t") >> the file x.csv has 1,411,190 conlumns titles "x231501" "X2315102".... >> can you please tell me what the meaning of columns? are they >> expression levels for all probesets? >> how can i get RMA expression level for each probe? > > What do you mean by this. Typically summarization is considered part > of the RMA method and after summarization you have probeset level > values, not probe level values. > > Kasper > > >> >> Yuan >> >> >> Martin Morgan wrote: >> "James W. MacDonald" writes: >> >>> Hi Yuan, >>> >>> Jay an wrote: >>>> Hello, >>>> I got several .CEL files to do RMA using exonmap library below: >>>>> raw.data <- read.exon() >>>>> raw.data at cdfName <- "exon.pmcdf" >>>>> x.rma <- rma(raw.data) >>>>> write.table(x.rma, file="x.csv", sep="\t") >>> >>> I'm surprised that worked. If you want to write out the expression >> >> There's a method that converts an ExpressionSet into a data.frame, >> taking the transpose of the expression values and cbind'ing (adding as >> columns) the phenotypic data. >> >>> library(Biobase) >>> data(sample.ExpressionSet) >>> names(as(sample.ExpressionSet, "data.frame")) >> [1] "AFFX.MurIL2_at" "AFFX.MurIL10_at" >> [3] "AFFX.MurIL4_at" "AFFX.MurFAS_at" >> [5] "AFFX.BioB.5_at" "AFFX.BioB.M_at" >> ... >> [499] "X31738_at" "X31739_at" >> [501] "sex" "type" >> [503] "score" >> >> This gets invoked by write.table and other functions that try to >> coerce their arguments to a data.frame. This can be convenient for >> instance in machine learning, where you can write a formula with '.' >> to indicate 'all columns' of a data.frame, and just provide the >> (probably filtered) ExpressionSet as the data argument. >> >> The affyPLM package might help to 'get RMA expression levels for each >> probe'. >> >> Martin >> >>> values you want to use write.exprs(), not write.table(), which is >>> intended to write out data.frames or matrices (and x.rma is neither). >>> >>> Best, >>> >>> Jim >>> >>> >>>> the file x.csv has 1,411,190 conlumns titles "x231501" >>>> "X2315102".... >>>> can you please tell me what the meaning of columns? are they >>>> expression levels for all probesets? >>>> how can i get RMA expression level for each probe? >>>> >>>> >>>> thanks >>>> Yuan >>>> >>>> >>>> >>>> >>>> --------------------------------- >>>> >>>> [[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 >>> >>> -- >>> 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 >>> >>> _______________________________________________ >>> 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 >> >> -- >> Martin Morgan >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M2 B169 >> Phone: (206) 667-2793 >> >> >> >> --------------------------------- >> >> >> --------------------------------- >> >> [[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 > > > > > --------------------------------- > > > --------------------------------- > > [[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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
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Hi, If you have a copy of the X:Map database installed and exonmap set up properly, then a call to probeset.to.transcript(X), where X is a list of probeset ids, will give you a transcript list back... See ?probeset.to.transcript and the vignette for more details... cheers Crispin On 21/1/08 11:41, "Jay an" <jayuan2007 at="" yahoo.com=""> wrote: > Martin, Thanks. > the corresponding between probeset and probe can be obtained by using > mget(featurenames(x.rma), exon.pmcdf). my another question is: > is there a way to get corresponding between transcripts > and probesets? > > thanks > Yuan > > -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:13}}
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Yuan Jian ▴ 250
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Hi, Did you install the whole Ensembl Homo_spaiens core database before you installed X:Map? We don't use all the tables in Ensembl but it is complex enough to make it generally easier just to install the whole database rather than to try to install bits of it. Crispin On 22/1/08 02:39, "Yuan Jian" <jayuan2008 at="" yahoo.com=""> wrote: > Hi Crispin, > > 1/ > I installed xmap database in my localhost. > but when I ask for transcript for a probeset. it always returns NULL or NA. > >> xmapDatabase("Human") > done. >> probeset.to.transcript("3102379") > [1] NA >> probeset.to.transcript("1112997") > NULL >> probeset.to.transcript("3933543") > [1] NA >> probeset.to.transcript("3102411") > [1] NA >> probeset.to.transcript("3102443") > [1] NA >> probeset.to.transcript("2315101") > NULL > > for the function of probe.to.transcript, which tables in > xmap_homo_sapiens_core_47_36i have been used? > > 2/ > in mysql database, I found probeset_id=1427856 has 7120 probes. > does this probeset has really so many probes? > in R I can not find probes for this probeset as below: > >> probeset.to.probe("1427856") > NULL > > is there anything wrong in my installation or using? > > thanks > Yuan > > > > ----- Original Message ---- > From: Crispin Miller <cmiller at="" picr.man.ac.uk=""> > To: Jay an <jayuan2007 at="" yahoo.com=""> > Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Sent: Tuesday, January 22, 2008 1:19:49 AM > Subject: Re: [BioC] exonmap RMA function > > > Hi, > If you have a copy of the X:Map database installed and exonmap set up > properly, then a call to probeset.to.transcript(X), where X is a list > of > probeset ids, will give you a transcript list back... > > See ?probeset.to.transcript and the vignette for more details... > > cheers > Crispin > > > > > > On 21/1/08 11:41, "Jay an" <jayuan2007 at="" yahoo.com=""> wrote: > >> Martin, Thanks. >> the corresponding between probeset and probe can be obtained by using >> mget(featurenames(x.rma), exon.pmcdf). my another question is: >> is there a way to get corresponding between transcripts >> and probesets? >> >> thanks >> Yuan >> >> > > -------------------------------------------------------- > > > This email is confidential and intended solely for the...{{dropped:26}}
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Yuan Jian ▴ 250
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Hi, No! You've only downloaded the X:Map part of the setup. Before you do that, you need to download Ensembl and install that separately, first. Have a look at INSTALL.TXT file in the xmap download, which tells you how to set it up... Crispin On 22/1/08 13:36, "Yuan Jian" <jayuan2008 at="" yahoo.com=""> wrote: > 1/ > I followed your instruction to install database. > which was downloaded xmap_homo_sapiens_core_47_36i.tgz > from your web page http://xmap.picr.man.ac.uk/download/. > is it the whole Ensembl Homo_sapaiens database? > > 2/ > which tables are accessed in function probeset.to.transcript? > > regards > > Yuan > > > > ----- Original Message ---- > From: Crispin Miller <cmiller at="" picr.man.ac.uk=""> > To: Yuan Jian <jayuan2008 at="" yahoo.com=""> > Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Sent: Tuesday, January 22, 2008 7:08:17 PM > Subject: Re: [BioC] exonmap RMA function > > > Hi, > Did you install the whole Ensembl Homo_spaiens core database before you > installed X:Map? > > We don't use all the tables in Ensembl but it is complex enough to make > it > generally easier just to install the whole database rather than to try > to > install bits of it. > > Crispin > > > > -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:13}}
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