For the record, replying to the list. Yes, order is preserved. B
On Jun 27, 2012 10:08 PM, "Cindy [guest]" <guest@bioconductor.org> wrote:

>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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