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}}
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
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
--
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
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
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
>
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
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