Bionconductor help

Hi,

You would get better response if you post at Bioconductor mailing list.
http://www.bioconductor.org/help/mailing-list/

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)")
}

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 ) {

   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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