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Bionconductor help

3 messages · Payal Urs, arun, Martin Morgan

arun
# 
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.urs at gmail.com>
To: r-help at 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

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Martin Morgan
#
On 06/07/2013 07:16 AM, arun wrote:
Agreed, though in this case I think
...
what needs to happen here is that the return value needs to be assigned to a 
variable,

     Data <- ReadAffyData(name)

Martin
...