[BioC] Subsetting in xps

Michael Walter michael.walter at med.uni-tuebingen.de
Fri Nov 6 13:19:19 CET 2009


Dear all,

I'm using xps to read Affy gene array cel files. If the number of arrays is exceeding 15 arrays I can no longer look at the feature data due to memory limitations. So I'd like to generate a root tree for the entire study and then look at the values for a subset for QC. I can generate a data tree set with the intensities of only a fraction by specifing the sample names (please see code and sessionInfo below). However, when I subsequently run RMA on the newly generated tree the resulting data frame contains all samples from the initial root tree. The code here is a small example with 4 arrays for demo purposes. If anyone has a suggestion, how to obtain the normalized signales from my subset, I would be very happy.

Kind regards,

Michael



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> library(RColorBrewer)
> library(xps)

Welcome to xps version 1.4.6 
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2009 by Christian Stratowa
    

Attache Paket: 'xps'


        The following object(s) are masked from package:Biobase :

         exprs,
         exprs<-,
         se.exprs 

> 
> project = "M9R_001"

> celfile = getwd()

> filenames = list.files(path=celfile)

> filenames = filenames[grep(".CEL", filenames)]

> filenames

[1] "M9R_001c01_1_(HuGene-1_0-st-v1).CEL" "M9R_001c02_1_(HuGene-1_0-st-v1).CEL"

[3] "M9R_001c03_1_(HuGene-1_0-st-v1).CEL" "M9R_001c04_1_(HuGene-1_0-st-v1).CEL"

> scheme.HuGene10 <- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes","Scheme_HuGene10stv1r4_na27_2.root",sep="/"))

> data.xps <- root.data(scheme.HuGene10, 
+ paste(getwd(), paste(project, "_cel.root", sep=""), sep="/"))

> fname.tree = data.xps at treenames

> data <- attachMask(data.xps)

> data <- attachInten(data.xps, treenames=unlist(fname.tree[1:3]))

> head(data at data)
  X Y M9R_001c01_1_(HuGene-1_0-st-v1).cel_MEAN
1 0 0                                     6745
2 1 0                                      124
3 2 0                                     6719
4 3 0                                       90
5 4 0                                       61
6 5 0                                       89

  M9R_001c02_1_(HuGene-1_0-st-v1).cel_MEAN
1                                     8246
2                                      127
3                                     8231
4                                      122
5                                       61
6                                      127

  M9R_001c03_1_(HuGene-1_0-st-v1).cel_MEAN
1                                     6190
2                                      112
3                                     5958
4                                       72
5                                       68
6                                      116

> dim(data at data)

[1] 1102500       5

> data.rma <- rma(data, "tmpdt_dataRMA", background="antigenomic", normalize=T, 
+ exonlevel=c(402492,402492,402492), verbose = FALSE)

> expr.rma <- validData(data.rma)

> dim(expr.rma)

[1] 33025     4

> sessionInfo()

R version 2.9.0 (2009-04-17) 
i386-pc-mingw32 

locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] xps_1.4.6          RColorBrewer_1.0-2 Biobase_2.4.1      ROC_1.18.0        
> 


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