Dist of exprSet object
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Marcus Davy ▴ 680
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P 17 of the vignette("affy"). e.g. chipCols <- rainbow(ncol(exprs(affybatch.example))) boxplot(affybatch.example, col=chipCols) Marcus On 7/27/06 10:40 AM, "Marco Blanchette" <mblanche at="" berkeley.edu=""> wrote: > Thank you all, > > Using bioclite to download the annotation fixed the problem. > > Now, I am getting into simpler R problem. I have an exprSet object of 4 > arrays: >> eset > Expression Set (exprSet) with > 18952 genes > 4 samples > phenoData object with 1 variables and 4 cases > varLabels > sample: arbitrary numbering > > My goal is to draw a boxplot of the 4 different samples. Surely I can do: >> boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3], exprs(eset)[,4], > col=c(2,3,4,5)) > > But is there an easier way to do with without having to subscript each > individual column? [right now I have only 4 but when I will have 20, I?ll > get bored quite rapidly] > > Sorry if this sounds easy, I am still learning the basics of R > > Marco > ______________________________ > Marco Blanchette, Ph.D. > > mblanche at uclink.berkeley.edu > > Donald C. Rio's lab > Department of Molecular and Cell Biology > 16 Barker Hall > University of California > Berkeley, CA 94720-3204 > > Tel: (510) 642-1084 > Cell: (510) 847-0996 > Fax: (510) 642-6062 ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}
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Actually you need affyPLM loaded to boxplot an exprSet. affy only provides the method for AffyBatch objects. Otherwise your example is correct. Best, Ben eg ..... > library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: affyio > library(affydata) > data(Dilution) > eset <- rma(Dilution) Background correcting Normalizing Calculating Expression > boxplot(eset) # throws error Error in boxplot.default(eset) : invalid first argument > library(affyPLM) Loading required package: gcrma Loading required package: matchprobes > boxplot(eset) #works fine. On Thu, 2006-07-27 at 10:58 +1200, Marcus Davy wrote: > P 17 of the vignette("affy"). > > e.g. > > chipCols <- rainbow(ncol(exprs(affybatch.example))) > boxplot(affybatch.example, col=chipCols) > > Marcus > > > On 7/27/06 10:40 AM, "Marco Blanchette" <mblanche at="" berkeley.edu=""> wrote: > > > Thank you all, > > > > Using bioclite to download the annotation fixed the problem. > > > > Now, I am getting into simpler R problem. I have an exprSet object of 4 > > arrays: > >> eset > > Expression Set (exprSet) with > > 18952 genes > > 4 samples > > phenoData object with 1 variables and 4 cases > > varLabels > > sample: arbitrary numbering > > > > My goal is to draw a boxplot of the 4 different samples. Surely I can do: > >> boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3], exprs(eset)[,4], > > col=c(2,3,4,5)) > > > > But is there an easier way to do with without having to subscript each > > individual column? [right now I have only 4 but when I will have 20, I?ll > > get bored quite rapidly] > > > > Sorry if this sounds easy, I am still learning the basics of R > > > > Marco > > ______________________________ > > Marco Blanchette, Ph.D. > > > > mblanche at uclink.berkeley.edu > > > > Donald C. Rio's lab > > Department of Molecular and Cell Biology > > 16 Barker Hall > > University of California > > Berkeley, CA 94720-3204 > > > > Tel: (510) 642-1084 > > Cell: (510) 847-0996 > > Fax: (510) 642-6062 > > > ______________________________________________________ > > The contents of this e-mail are privileged and/or confidenti...{{dropped}} > > _______________________________________________ > 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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Hum... This exemplified my hate-love relationship that I have with R... Very powerful, but very difficult to master... One more issue. Each experiments are in duplicates (2 experiments, 2 replicates -> 4 arrays). My goal is to partition the distribution in genes in the 10% top most expressed, 10% to 20% most expressed, 20% to 30% most expressed, and so on. eset is my exprSet object containing the rma computed expression for each gene on the 4 arrays: > eset Expression Set (exprSet) with 18952 genes 4 samples phenoData object with 1 variables and 4 cases varLabels sample: arbitrary numbering So I need to: 1) Get the average expression for each gene from the 2 replicates Would you do: >exp1 = iter(eset[,1,2], , mean) >exp2 = iter(eset[,2,3], , mean) Or is there a better way? 2) Break down the distribution per 10% bin as in >top10 = geneNames(eset)[(rank(exp1) >= 0*(length(exp1)/10) & rank(exp1) < 1*(length(exp1)/10))] >top10_20 = geneNames(eset)[(rank(exp1) >= 1*(length(exp1)/10) & rank(exp1) < 2*(length(exp1)/10))] top20_30 = geneNames(eset)[(rank(exp1) >= 2*(length(exp1)/10) & rank(exp1) < 3*(length(exp1)/10))] Or is there a better way? [I'm pretty sure there a more R elegant way than that...] Many thanks folks Cheers, Marco On 7/26/06 4:05 PM, "Ben Bolstad" <bmb at="" bmbolstad.com=""> wrote: > Actually you need affyPLM loaded to boxplot an exprSet. affy only > provides the method for AffyBatch objects. Otherwise your example is > correct. > > Best, > > Ben > > > eg ..... > >> library(affy) > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > > Vignettes contain introductory material. > > To view, simply type 'openVignette()' or start with 'help(Biobase)'. > > For details on reading vignettes, see the openVignette help page. > > > Loading required package: affyio >> library(affydata) >> data(Dilution) >> eset <- rma(Dilution) > Background correcting > Normalizing > Calculating Expression >> boxplot(eset) # throws error > Error in boxplot.default(eset) : invalid first argument >> library(affyPLM) > Loading required package: gcrma > Loading required package: matchprobes >> boxplot(eset) #works fine. > > > > > > > > > On Thu, 2006-07-27 at 10:58 +1200, Marcus Davy wrote: >> P 17 of the vignette("affy"). >> >> e.g. >> >> chipCols <- rainbow(ncol(exprs(affybatch.example))) >> boxplot(affybatch.example, col=chipCols) >> >> Marcus >> >> >> On 7/27/06 10:40 AM, "Marco Blanchette" <mblanche at="" berkeley.edu=""> wrote: >> >>> Thank you all, >>> >>> Using bioclite to download the annotation fixed the problem. >>> >>> Now, I am getting into simpler R problem. I have an exprSet object of 4 >>> arrays: >>>> eset >>> Expression Set (exprSet) with >>> 18952 genes >>> 4 samples >>> phenoData object with 1 variables and 4 cases >>> varLabels >>> sample: arbitrary numbering >>> >>> My goal is to draw a boxplot of the 4 different samples. Surely I can do: >>>> boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3], >>>> exprs(eset)[,4], >>> col=c(2,3,4,5)) >>> >>> But is there an easier way to do with without having to subscript each >>> individual column? [right now I have only 4 but when I will have 20, I?ll >>> get bored quite rapidly] >>> >>> Sorry if this sounds easy, I am still learning the basics of R >>> >>> Marco >>> ______________________________ >>> Marco Blanchette, Ph.D. >>> >>> mblanche at uclink.berkeley.edu >>> >>> Donald C. Rio's lab >>> Department of Molecular and Cell Biology >>> 16 Barker Hall >>> University of California >>> Berkeley, CA 94720-3204 >>> >>> Tel: (510) 642-1084 >>> Cell: (510) 847-0996 >>> Fax: (510) 642-6062 >> >> >> ______________________________________________________ >> >> The contents of this e-mail are privileged and/or confidenti...{{dropped}} >> >> _______________________________________________ >> 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 > ______________________________ Marco Blanchette, Ph.D. mblanche at uclink.berkeley.edu Donald C. Rio's lab Department of Molecular and Cell Biology 16 Barker Hall University of California Berkeley, CA 94720-3204 Tel: (510) 642-1084 Cell: (510) 847-0996 Fax: (510) 642-6062 --
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Hi Marco, 1) have a look at "rowMeans" 2) have a look at the functions "cut" and "split" x = rnorm(100) ct = cut(rank(x), 10) sp = split(x, ct) boxplot(sp) Cheers Wolfgang > Hum... This exemplified my hate-love relationship that I have with R... Very > powerful, but very difficult to master... > > One more issue. Each experiments are in duplicates (2 experiments, 2 > replicates -> 4 arrays). My goal is to partition the distribution in genes > in the 10% top most expressed, 10% to 20% most expressed, 20% to 30% most > expressed, and so on. > > eset is my exprSet object containing the rma computed expression for each > gene on the 4 arrays: >> eset > Expression Set (exprSet) with > 18952 genes > 4 samples > phenoData object with 1 variables and 4 cases > varLabels > sample: arbitrary numbering > > So I need to: > > 1) Get the average expression for each gene from the 2 replicates > Would you do: >> exp1 = iter(eset[,1,2], , mean) >> exp2 = iter(eset[,2,3], , mean) > > Or is there a better way? > > 2) Break down the distribution per 10% bin as in >> top10 = geneNames(eset)[(rank(exp1) >= 0*(length(exp1)/10) & rank(exp1) < > 1*(length(exp1)/10))] >> top10_20 = geneNames(eset)[(rank(exp1) >= 1*(length(exp1)/10) & rank(exp1) < > 2*(length(exp1)/10))] > top20_30 = geneNames(eset)[(rank(exp1) >= 2*(length(exp1)/10) & rank(exp1) < > 3*(length(exp1)/10))] > > Or is there a better way? [I'm pretty sure there a more R elegant way than > that...] > > Many thanks folks > > Cheers, > > Marco > > > On 7/26/06 4:05 PM, "Ben Bolstad" <bmb at="" bmbolstad.com=""> wrote: > >> Actually you need affyPLM loaded to boxplot an exprSet. affy only >> provides the method for AffyBatch objects. Otherwise your example is >> correct. >> >> Best, >> >> Ben >> >> >> eg ..... >> >>> library(affy) >> Loading required package: Biobase >> Loading required package: tools >> >> Welcome to Bioconductor >> >> >> Vignettes contain introductory material. >> >> To view, simply type 'openVignette()' or start with 'help(Biobase)'. >> >> For details on reading vignettes, see the openVignette help page. >> >> >> Loading required package: affyio >>> library(affydata) >>> data(Dilution) >>> eset <- rma(Dilution) >> Background correcting >> Normalizing >> Calculating Expression >>> boxplot(eset) # throws error >> Error in boxplot.default(eset) : invalid first argument >>> library(affyPLM) >> Loading required package: gcrma >> Loading required package: matchprobes >>> boxplot(eset) #works fine. >> >> >> >> >> >> >> >> On Thu, 2006-07-27 at 10:58 +1200, Marcus Davy wrote: >>> P 17 of the vignette("affy"). >>> >>> e.g. >>> >>> chipCols <- rainbow(ncol(exprs(affybatch.example))) >>> boxplot(affybatch.example, col=chipCols) >>> >>> Marcus >>> >>> >>> On 7/27/06 10:40 AM, "Marco Blanchette" <mblanche at="" berkeley.edu=""> wrote: >>> >>>> Thank you all, >>>> >>>> Using bioclite to download the annotation fixed the problem. >>>> >>>> Now, I am getting into simpler R problem. I have an exprSet object of 4 >>>> arrays: >>>>> eset >>>> Expression Set (exprSet) with >>>> 18952 genes >>>> 4 samples >>>> phenoData object with 1 variables and 4 cases >>>> varLabels >>>> sample: arbitrary numbering >>>> >>>> My goal is to draw a boxplot of the 4 different samples. Surely I can do: >>>>> boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3], >>>>> exprs(eset)[,4], >>>> col=c(2,3,4,5)) >>>> >>>> But is there an easier way to do with without having to subscript each >>>> individual column? [right now I have only 4 but when I will have 20, I?ll >>>> get bored quite rapidly] >>>> >>>> Sorry if this sounds easy, I am still learning the basics of R >>>> >>>> Marco >>>> ______________________________ >>>> Marco Blanchette, Ph.D. >>>> >>>> mblanche at uclink.berkeley.edu >>>> >>>> Donald C. Rio's lab >>>> Department of Molecular and Cell Biology >>>> 16 Barker Hall >>>> University of California >>>> Berkeley, CA 94720-3204 >>>> >>>> Tel: (510) 642-1084 >>>> Cell: (510) 847-0996 >>>> Fax: (510) 642-6062 >>> >>> ______________________________________________________ >>> >>> The contents of this e-mail are privileged and/or confidenti...{{dropped}} >>> >>> _______________________________________________ >>> 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 > > ______________________________ > Marco Blanchette, Ph.D. > > mblanche at uclink.berkeley.edu > > Donald C. Rio's lab > Department of Molecular and Cell Biology > 16 Barker Hall > University of California > Berkeley, CA 94720-3204 > > Tel: (510) 642-1084 > Cell: (510) 847-0996 > Fax: (510) 642-6062 > -- > > _______________________________________________ > 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 -- ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
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Can't find any info on rawMeans: > ?rawMeans No documentation for 'rawMeans' in specified packages and libraries: you could try 'help.search("rawMeans")' On 7/27/06 2:00 AM, "Wolfgang Huber" <huber at="" ebi.ac.uk=""> wrote: > Hi Marco, > > 1) have a look at "rowMeans" > > 2) have a look at the functions "cut" and "split" > > x = rnorm(100) > ct = cut(rank(x), 10) > sp = split(x, ct) > boxplot(sp) > > > Cheers > Wolfgang > >> Hum... This exemplified my hate-love relationship that I have with R... Very >> powerful, but very difficult to master... >> >> One more issue. Each experiments are in duplicates (2 experiments, 2 >> replicates -> 4 arrays). My goal is to partition the distribution in genes >> in the 10% top most expressed, 10% to 20% most expressed, 20% to 30% most >> expressed, and so on. >> >> eset is my exprSet object containing the rma computed expression for each >> gene on the 4 arrays: >>> eset >> Expression Set (exprSet) with >> 18952 genes >> 4 samples >> phenoData object with 1 variables and 4 cases >> varLabels >> sample: arbitrary numbering >> >> So I need to: >> >> 1) Get the average expression for each gene from the 2 replicates >> Would you do: >>> exp1 = iter(eset[,1,2], , mean) >>> exp2 = iter(eset[,2,3], , mean) >> >> Or is there a better way? >> >> 2) Break down the distribution per 10% bin as in >>> top10 = geneNames(eset)[(rank(exp1) >= 0*(length(exp1)/10) & rank(exp1) < >> 1*(length(exp1)/10))] >>> top10_20 = geneNames(eset)[(rank(exp1) >= 1*(length(exp1)/10) & rank(exp1) < >> 2*(length(exp1)/10))] >> top20_30 = geneNames(eset)[(rank(exp1) >= 2*(length(exp1)/10) & rank(exp1) < >> 3*(length(exp1)/10))] >> >> Or is there a better way? [I'm pretty sure there a more R elegant way than >> that...] >> >> Many thanks folks >> >> Cheers, >> >> Marco >> >> >> On 7/26/06 4:05 PM, "Ben Bolstad" <bmb at="" bmbolstad.com=""> wrote: >> >>> Actually you need affyPLM loaded to boxplot an exprSet. affy only >>> provides the method for AffyBatch objects. Otherwise your example is >>> correct. >>> >>> Best, >>> >>> Ben >>> >>> >>> eg ..... >>> >>>> library(affy) >>> Loading required package: Biobase >>> Loading required package: tools >>> >>> Welcome to Bioconductor >>> >>> >>> Vignettes contain introductory material. >>> >>> To view, simply type 'openVignette()' or start with 'help(Biobase)'. >>> >>> For details on reading vignettes, see the openVignette help page. >>> >>> >>> Loading required package: affyio >>>> library(affydata) >>>> data(Dilution) >>>> eset <- rma(Dilution) >>> Background correcting >>> Normalizing >>> Calculating Expression >>>> boxplot(eset) # throws error >>> Error in boxplot.default(eset) : invalid first argument >>>> library(affyPLM) >>> Loading required package: gcrma >>> Loading required package: matchprobes >>>> boxplot(eset) #works fine. >>> >>> >>> >>> >>> >>> >>> >>> On Thu, 2006-07-27 at 10:58 +1200, Marcus Davy wrote: >>>> P 17 of the vignette("affy"). >>>> >>>> e.g. >>>> >>>> chipCols <- rainbow(ncol(exprs(affybatch.example))) >>>> boxplot(affybatch.example, col=chipCols) >>>> >>>> Marcus >>>> >>>> >>>> On 7/27/06 10:40 AM, "Marco Blanchette" <mblanche at="" berkeley.edu=""> wrote: >>>> >>>>> Thank you all, >>>>> >>>>> Using bioclite to download the annotation fixed the problem. >>>>> >>>>> Now, I am getting into simpler R problem. I have an exprSet object of 4 >>>>> arrays: >>>>>> eset >>>>> Expression Set (exprSet) with >>>>> 18952 genes >>>>> 4 samples >>>>> phenoData object with 1 variables and 4 cases >>>>> varLabels >>>>> sample: arbitrary numbering >>>>> >>>>> My goal is to draw a boxplot of the 4 different samples. Surely I can do: >>>>>> boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3], >>>>>> exprs(eset)[,4], >>>>> col=c(2,3,4,5)) >>>>> >>>>> But is there an easier way to do with without having to subscript each >>>>> individual column? [right now I have only 4 but when I will have 20, I?ll >>>>> get bored quite rapidly] >>>>> >>>>> Sorry if this sounds easy, I am still learning the basics of R >>>>> >>>>> Marco >>>>> ______________________________ >>>>> Marco Blanchette, Ph.D. >>>>> >>>>> mblanche at uclink.berkeley.edu >>>>> >>>>> Donald C. Rio's lab >>>>> Department of Molecular and Cell Biology >>>>> 16 Barker Hall >>>>> University of California >>>>> Berkeley, CA 94720-3204 >>>>> >>>>> Tel: (510) 642-1084 >>>>> Cell: (510) 847-0996 >>>>> Fax: (510) 642-6062 >>>> >>>> ______________________________________________________ >>>> >>>> The contents of this e-mail are privileged and/or confidenti...{{dropped}} >>>> >>>> _______________________________________________ >>>> 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 >> >> ______________________________ >> Marco Blanchette, Ph.D. >> >> mblanche at uclink.berkeley.edu >> >> Donald C. Rio's lab >> Department of Molecular and Cell Biology >> 16 Barker Hall >> University of California >> Berkeley, CA 94720-3204 >> >> Tel: (510) 642-1084 >> Cell: (510) 847-0996 >> Fax: (510) 642-6062 >> -- >> >> _______________________________________________ >> 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 > Marco Blanchette, Ph.D. mblanche at berkeley.edu Donald C. Rio's lab Department of Molecular and Cell Biology 16 Barker Hall University of California Berkeley, CA 94720-3204 Tel: (510) 642-1084 Cell: (510) 847-0996 Fax: (510) 642-6062
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Hi Marco, you made a little typo, the function is rowMeans, not rawMeans. Francois On Thu, 2006-07-27 at 10:54 -0700, Marco Blanchette wrote: > Can't find any info on rawMeans: > > > ?rawMeans > No documentation for 'rawMeans' in specified packages and libraries: > you could try 'help.search("rawMeans")' > > > On 7/27/06 2:00 AM, "Wolfgang Huber" <huber at="" ebi.ac.uk=""> wrote: > > > Hi Marco, > > > > 1) have a look at "rowMeans" > > > > 2) have a look at the functions "cut" and "split" > > > > x = rnorm(100) > > ct = cut(rank(x), 10) > > sp = split(x, ct) > > boxplot(sp) > > > > > > Cheers > > Wolfgang > > > >> Hum... This exemplified my hate-love relationship that I have with R... Very > >> powerful, but very difficult to master... > >> > >> One more issue. Each experiments are in duplicates (2 experiments, 2 > >> replicates -> 4 arrays). My goal is to partition the distribution in genes > >> in the 10% top most expressed, 10% to 20% most expressed, 20% to 30% most > >> expressed, and so on. > >> > >> eset is my exprSet object containing the rma computed expression for each > >> gene on the 4 arrays: > >>> eset > >> Expression Set (exprSet) with > >> 18952 genes > >> 4 samples > >> phenoData object with 1 variables and 4 cases > >> varLabels > >> sample: arbitrary numbering > >> > >> So I need to: > >> > >> 1) Get the average expression for each gene from the 2 replicates > >> Would you do: > >>> exp1 = iter(eset[,1,2], , mean) > >>> exp2 = iter(eset[,2,3], , mean) > >> > >> Or is there a better way? > >> > >> 2) Break down the distribution per 10% bin as in > >>> top10 = geneNames(eset)[(rank(exp1) >= 0*(length(exp1)/10) & rank(exp1) < > >> 1*(length(exp1)/10))] > >>> top10_20 = geneNames(eset)[(rank(exp1) >= 1*(length(exp1)/10) & rank(exp1) < > >> 2*(length(exp1)/10))] > >> top20_30 = geneNames(eset)[(rank(exp1) >= 2*(length(exp1)/10) & rank(exp1) < > >> 3*(length(exp1)/10))] > >> > >> Or is there a better way? [I'm pretty sure there a more R elegant way than > >> that...] > >> > >> Many thanks folks > >> > >> Cheers, > >> > >> Marco > >> > >> > >> On 7/26/06 4:05 PM, "Ben Bolstad" <bmb at="" bmbolstad.com=""> wrote: > >> > >>> Actually you need affyPLM loaded to boxplot an exprSet. affy only > >>> provides the method for AffyBatch objects. Otherwise your example is > >>> correct. > >>> > >>> Best, > >>> > >>> Ben > >>> > >>> > >>> eg ..... > >>> > >>>> library(affy) > >>> Loading required package: Biobase > >>> Loading required package: tools > >>> > >>> Welcome to Bioconductor > >>> > >>> > >>> Vignettes contain introductory material. > >>> > >>> To view, simply type 'openVignette()' or start with 'help(Biobase)'. > >>> > >>> For details on reading vignettes, see the openVignette help page. > >>> > >>> > >>> Loading required package: affyio > >>>> library(affydata) > >>>> data(Dilution) > >>>> eset <- rma(Dilution) > >>> Background correcting > >>> Normalizing > >>> Calculating Expression > >>>> boxplot(eset) # throws error > >>> Error in boxplot.default(eset) : invalid first argument > >>>> library(affyPLM) > >>> Loading required package: gcrma > >>> Loading required package: matchprobes > >>>> boxplot(eset) #works fine. > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> On Thu, 2006-07-27 at 10:58 +1200, Marcus Davy wrote: > >>>> P 17 of the vignette("affy"). > >>>> > >>>> e.g. > >>>> > >>>> chipCols <- rainbow(ncol(exprs(affybatch.example))) > >>>> boxplot(affybatch.example, col=chipCols) > >>>> > >>>> Marcus > >>>> > >>>> > >>>> On 7/27/06 10:40 AM, "Marco Blanchette" <mblanche at="" berkeley.edu=""> wrote: > >>>> > >>>>> Thank you all, > >>>>> > >>>>> Using bioclite to download the annotation fixed the problem. > >>>>> > >>>>> Now, I am getting into simpler R problem. I have an exprSet object of 4 > >>>>> arrays: > >>>>>> eset > >>>>> Expression Set (exprSet) with > >>>>> 18952 genes > >>>>> 4 samples > >>>>> phenoData object with 1 variables and 4 cases > >>>>> varLabels > >>>>> sample: arbitrary numbering > >>>>> > >>>>> My goal is to draw a boxplot of the 4 different samples. Surely I can do: > >>>>>> boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3], > >>>>>> exprs(eset)[,4], > >>>>> col=c(2,3,4,5)) > >>>>> > >>>>> But is there an easier way to do with without having to subscript each > >>>>> individual column? [right now I have only 4 but when I will have 20, I?ll > >>>>> get bored quite rapidly] > >>>>> > >>>>> Sorry if this sounds easy, I am still learning the basics of R > >>>>> > >>>>> Marco > >>>>> ______________________________ > >>>>> Marco Blanchette, Ph.D. > >>>>> > >>>>> mblanche at uclink.berkeley.edu > >>>>> > >>>>> Donald C. Rio's lab > >>>>> Department of Molecular and Cell Biology > >>>>> 16 Barker Hall > >>>>> University of California > >>>>> Berkeley, CA 94720-3204 > >>>>> > >>>>> Tel: (510) 642-1084 > >>>>> Cell: (510) 847-0996 > >>>>> Fax: (510) 642-6062 > >>>> > >>>> ______________________________________________________ > >>>> > >>>> The contents of this e-mail are privileged and/or confidenti...{{dropped}} > >>>> > >>>> _______________________________________________ > >>>> 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 > >> > >> ______________________________ > >> Marco Blanchette, Ph.D. > >> > >> mblanche at uclink.berkeley.edu > >> > >> Donald C. Rio's lab > >> Department of Molecular and Cell Biology > >> 16 Barker Hall > >> University of California > >> Berkeley, CA 94720-3204 > >> > >> Tel: (510) 642-1084 > >> Cell: (510) 847-0996 > >> Fax: (510) 642-6062 > >> -- > >> > >> _______________________________________________ > >> 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 > > > > > Marco Blanchette, Ph.D. > > mblanche at berkeley.edu > > Donald C. Rio's lab > Department of Molecular and Cell Biology > 16 Barker Hall > University of California > Berkeley, CA 94720-3204 > > Tel: (510) 642-1084 > Cell: (510) 847-0996 > Fax: (510) 642-6062 > > _______________________________________________ > 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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You don't really need affyPLM. The problem is that the boxplot method for a matrix just gives you one big box, instead of a boxplot for each column. However, the boxplot method for a data.frame _will_ give you a box for each column. boxplot(as.data.frame(exprs(eset))) Best, Jim Ben Bolstad wrote: > Actually you need affyPLM loaded to boxplot an exprSet. affy only > provides the method for AffyBatch objects. Otherwise your example is > correct. > > Best, > > Ben > > > eg ..... > > >>library(affy) > > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > > Vignettes contain introductory material. > > To view, simply type 'openVignette()' or start with 'help(Biobase)'. > > For details on reading vignettes, see the openVignette help page. > > > Loading required package: affyio > >>library(affydata) >>data(Dilution) >>eset <- rma(Dilution) > > Background correcting > Normalizing > Calculating Expression > >>boxplot(eset) # throws error > > Error in boxplot.default(eset) : invalid first argument > >>library(affyPLM) > > Loading required package: gcrma > Loading required package: matchprobes > >>boxplot(eset) #works fine. > > > > > > > > > > On Thu, 2006-07-27 at 10:58 +1200, Marcus Davy wrote: > >>P 17 of the vignette("affy"). >> >>e.g. >> >>chipCols <- rainbow(ncol(exprs(affybatch.example))) >>boxplot(affybatch.example, col=chipCols) >> >>Marcus >> >> >>On 7/27/06 10:40 AM, "Marco Blanchette" <mblanche at="" berkeley.edu=""> wrote: >> >> >>>Thank you all, >>> >>>Using bioclite to download the annotation fixed the problem. >>> >>>Now, I am getting into simpler R problem. I have an exprSet object of 4 >>>arrays: >>> >>>>eset >>> >>>Expression Set (exprSet) with >>> 18952 genes >>> 4 samples >>> phenoData object with 1 variables and 4 cases >>> varLabels >>> sample: arbitrary numbering >>> >>>My goal is to draw a boxplot of the 4 different samples. Surely I can do: >>> >>>>boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3], exprs(eset)[,4], >>> >>>col=c(2,3,4,5)) >>> >>>But is there an easier way to do with without having to subscript each >>>individual column? [right now I have only 4 but when I will have 20, I?ll >>>get bored quite rapidly] >>> >>>Sorry if this sounds easy, I am still learning the basics of R >>> >>>Marco >>>______________________________ >>>Marco Blanchette, Ph.D. >>> >>>mblanche at uclink.berkeley.edu >>> >>>Donald C. Rio's lab >>>Department of Molecular and Cell Biology >>>16 Barker Hall >>>University of California >>>Berkeley, CA 94720-3204 >>> >>>Tel: (510) 642-1084 >>>Cell: (510) 847-0996 >>>Fax: (510) 642-6062 >> >> >>______________________________________________________ >> >>The contents of this e-mail are privileged and/or confidenti...{{dropped}} >> >>_______________________________________________ >>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 > > > _______________________________________________ > 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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