[R] Bionconductor help

[Martin Morgan]

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.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
>
>      [[alternative HTML version deleted]]
>
> ______________________________________________
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>
>
> ______________________________________________
> R-help at r-project.org mailing list
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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.
>


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