[BioC] oligo: ordering of \"backgroundCorrect\" and \"normalize\" output values

[Cindy [guest]]

Dear Bioconductor team,

I am currently using the oligo package for analyzing tiling array data (Affymetrix GeneChip Human Tiling 2.0R Array). I have already built a design platform using PlatformDesign package and was able to read in the raw .CEL files. I guess my question is when I use backgroundCorrect and normalize functions for data pre-processing, I get just the values back and no labels (as shown below: str(normalized)). Can I assume that the ordering of the values is the same as the raw pm data that I input into the backgroundCorrect function? In other words, does the first value following background correction and normalization correspond to the input from probe "2566" and sample "1_10_(Hs35b_P02R_v01).CEL" (shown below in str(raw.pm)). Is there any way to bring out the labels for both the probes and the samples? Thank you very much for your time!

# load expression data
raw.data <- read.celfiles(cel.files);

# get intensity data for pm only
raw.pm <- pm(raw.data);

str(raw.pm)
 num [1:6003165, 1:200] 56 73 155 98 60 103 91 184 176 110 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:6003165] "2566" "2567" "2568" "2569" ...
  ..$ : chr [1:200] "1_10_(Hs35b_P02R_v01).CEL" "1_11_(Hs35b_P02R_v01).CEL" "1_12_(Hs35b_P02R_v01).CEL" "1_13_(Hs35b_P02R_v01).CEL" ...

# perform preprocessing using RMA
bgCorrected <- backgroundCorrect(raw.pm, method = "rma");
normalized  <- normalize(bgCorrected, method = "quantile");

str(normalized)
 num [1:6003165, 1:200] 18.4 42.2 178.9 79.7 24.2 ...


Best regards,
Cindy

 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] pd.hs35b.p02r.v01_0.0.1 RSQLite_0.11.1          DBI_0.2-5              
[4] affxparser_1.28.0       oligo_1.20.1            oligoClasses_1.18.0    

loaded via a namespace (and not attached):
 [1] Biobase_2.16.0        BiocGenerics_0.2.0    BiocInstaller_1.4.3  
 [4] Biostrings_2.24.1     IRanges_1.14.2        affyio_1.24.0        
 [7] bit_1.1-8             codetools_0.2-8       ff_2.2-6             
[10] foreach_1.4.0         iterators_1.0.6       preprocessCore_1.18.0
[13] splines_2.15.0        stats4_2.15.0         tools_2.15.0         
[16] zlibbioc_1.2.0

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