[R] Bionconductor help
Hi
I am trying to do some data analysis using R and Bioconductor. I have a
function to read my data called ReadAffyData and a function to plot the
data called preqc. I want to know if there is any way I can extract
information (read: Data) from the ReadAffyData function into preqc in order
to produce plots? I have not completely understood the inheritance in R and
I am getting errors similar to the one below. I am new to R and could do
with any help in this aspect!
ReadAffyData - function( filename ) {
require(affy)
require(annotate)
Cov - read.table( filename, sep=\t, header=1, quote=,
comment= )
if( ! all( c( Filename, Label, Repl, Trt ) %in% colnames( Cov )
) )
{
stop( Missing mandatory column )
}
Cov - Cov[order(Cov$Trt),]
i - table(Cov$Trt)
Cov$Repl - unlist( lapply( i, function( j ) 1:j ) )
Cov$Label - paste( as.character( Cov$Trt ), Cov$Repl, sep=: )
rownames(Cov) - as.character(Cov$Label)
tmp1 - colnames( Cov )
tmp2 - rep( , length( Cov ) )
for( i in 1:length( tmp2 ) )
{
tmp2[i] - paste( sort( unique( as.character( Cov[,i] ) ) ),
collapse=/ )
}
labelDescription - data.frame( labelDescription=tmp2 )
rownames( labelDescription ) - tmp1
tmp - new( AnnotatedDataFrame, data=Cov,
varMetadata=labelDescription)
Data - ReadAffy( sampleNames=as.character( Cov$Label
),phenoData=tmp, verbose=TRUE )
}
preQC - function(name){
ReadAffyData(name)
plotDensity( log2( pm( Data ) ), xlab=Log2( Intensity ), ylab=Density,
main=Raw(PM))
}
preQC(cov.txt)
1 reading C:/CEL/GSM311471.CEL ...instantiating an AffyBatch (intensity a
506944x24 matrix)...done.
Reading in : C:/CEL/GSM311471.CEL
Reading in : C:/CEL/GSM311472.CEL
Reading in : C:/CEL/GSM311473.CEL
Reading in : C:/CEL/GSM311474.CEL
Reading in : C:/CEL/GSM311475.CEL
.
.
.
Error in pm(Data) :
error in evaluating the argument 'object' in selecting a method for
function 'pm': Error: object 'Data' not found
sessionInf()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C LC_TIME=English_India.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
base
other attached packages:
[1] annotate_1.38.0 AnnotationDbi_1.22.6 affy_1.38.1
Biobase_2.20.0 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] affyio_1.28.0 BiocInstaller_1.10.1 DBI_0.2-7
IRanges_1.18.1preprocessCore_1.22.0
[6] RSQLite_0.11.4stats4_3.0.1 tools_3.0.1
XML_3.96-1.1 xtable_1.7-1
[11] zlibbioc_1.6.0
Thanking you,
Ipsitha
Graduate Student
London
[[alternative HTML version deleted]]
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Re: [R] Bionconductor help
Hi,
You would get better response if you post at Bioconductor mailing list.
http://www.bioconductor.org/help/mailing-list/
A.K.
- Original Message -
From: Payal Urs payal@gmail.com
To: r-help@r-project.org
Cc:
Sent: Friday, June 7, 2013 6:12 AM
Subject: [R] Bionconductor help
Hi
I am trying to do some data analysis using R and Bioconductor. I have a
function to read my data called ReadAffyData and a function to plot the
data called preqc. I want to know if there is any way I can extract
information (read: Data) from the ReadAffyData function into preqc in order
to produce plots? I have not completely understood the inheritance in R and
I am getting errors similar to the one below. I am new to R and could do
with any help in this aspect!
ReadAffyData - function( filename ) {
require(affy)
require(annotate)
Cov - read.table( filename, sep=\t, header=1, quote=,
comment= )
if( ! all( c( Filename, Label, Repl, Trt ) %in% colnames( Cov )
) )
{
stop( Missing mandatory column )
}
Cov - Cov[order(Cov$Trt),]
i - table(Cov$Trt)
Cov$Repl - unlist( lapply( i, function( j ) 1:j ) )
Cov$Label - paste( as.character( Cov$Trt ), Cov$Repl, sep=: )
rownames(Cov) - as.character(Cov$Label)
tmp1 - colnames( Cov )
tmp2 - rep( , length( Cov ) )
for( i in 1:length( tmp2 ) )
{
tmp2[i] - paste( sort( unique( as.character( Cov[,i] ) ) ),
collapse=/ )
}
labelDescription - data.frame( labelDescription=tmp2 )
rownames( labelDescription ) - tmp1
tmp - new( AnnotatedDataFrame, data=Cov,
varMetadata=labelDescription)
Data - ReadAffy( sampleNames=as.character( Cov$Label
),phenoData=tmp, verbose=TRUE )
}
preQC - function(name){
ReadAffyData(name)
plotDensity( log2( pm( Data ) ), xlab=Log2( Intensity ), ylab=Density,
main=Raw(PM))
}
preQC(cov.txt)
1 reading C:/CEL/GSM311471.CEL ...instantiating an AffyBatch (intensity a
506944x24 matrix)...done.
Reading in : C:/CEL/GSM311471.CEL
Reading in : C:/CEL/GSM311472.CEL
Reading in : C:/CEL/GSM311473.CEL
Reading in : C:/CEL/GSM311474.CEL
Reading in : C:/CEL/GSM311475.CEL
.
.
.
Error in pm(Data) :
error in evaluating the argument 'object' in selecting a method for
function 'pm': Error: object 'Data' not found
sessionInf()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C LC_TIME=English_India.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
base
other attached packages:
[1] annotate_1.38.0 AnnotationDbi_1.22.6 affy_1.38.1
Biobase_2.20.0 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] affyio_1.28.0 BiocInstaller_1.10.1 DBI_0.2-7
IRanges_1.18.1 preprocessCore_1.22.0
[6] RSQLite_0.11.4 stats4_3.0.1 tools_3.0.1
XML_3.96-1.1 xtable_1.7-1
[11] zlibbioc_1.6.0
Thanking you,
Ipsitha
Graduate Student
London
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bionconductor help
On 06/07/2013 07:16 AM, arun wrote:
Hi,
You would get better response if you post at Bioconductor mailing list.
http://www.bioconductor.org/help/mailing-list/
Agreed, though in this case I think
ReadAffyData - function( filename ) {
...
Data - ReadAffy( sampleNames=as.character( Cov$Label),
phenoData=tmp, verbose=TRUE )
}
preQC - function(name){
ReadAffyData(name)
what needs to happen here is that the return value needs to be assigned to a
variable,
Data - ReadAffyData(name)
Martin
plotDensity( log2( pm( Data ) ), xlab=Log2( Intensity ), ylab=Density,
main=Raw(PM))
}
A.K.
- Original Message -
From: Payal Urs payal@gmail.com
To: r-help@r-project.org
Cc:
Sent: Friday, June 7, 2013 6:12 AM
Subject: [R] Bionconductor help
Hi
I am trying to do some data analysis using R and Bioconductor. I have a
function to read my data called ReadAffyData and a function to plot the
data called preqc. I want to know if there is any way I can extract
information (read: Data) from the ReadAffyData function into preqc in order
to produce plots? I have not completely understood the inheritance in R and
I am getting errors similar to the one below. I am new to R and could do
with any help in this aspect!
ReadAffyData - function( filename ) {
...
Data - ReadAffy( sampleNames=as.character( Cov$Label ),phenoData=tmp,
verbose=TRUE )
}
preQC - function(name){
ReadAffyData(name)
plotDensity( log2( pm( Data ) ), xlab=Log2( Intensity ), ylab=Density,
main=Raw(PM))
}
preQC(cov.txt)
1 reading C:/CEL/GSM311471.CEL ...instantiating an AffyBatch (intensity a
506944x24 matrix)...done.
Reading in : C:/CEL/GSM311471.CEL
Reading in : C:/CEL/GSM311472.CEL
Reading in : C:/CEL/GSM311473.CEL
Reading in : C:/CEL/GSM311474.CEL
Reading in : C:/CEL/GSM311475.CEL
.
.
.
Error in pm(Data) :
error in evaluating the argument 'object' in selecting a method for
function 'pm': Error: object 'Data' not found
sessionInf()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C LC_TIME=English_India.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
base
other attached packages:
[1] annotate_1.38.0 AnnotationDbi_1.22.6 affy_1.38.1
Biobase_2.20.0 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] affyio_1.28.0 BiocInstaller_1.10.1 DBI_0.2-7
IRanges_1.18.1preprocessCore_1.22.0
[6] RSQLite_0.11.4stats4_3.0.1 tools_3.0.1
XML_3.96-1.1 xtable_1.7-1
[11] zlibbioc_1.6.0
Thanking you,
Ipsitha
Graduate Student
London
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Computational Biology / Fred Hutchinson Cancer Research Center
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Phone: (206) 667-2793
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
