oligo: ordering of \"backgroundCorrect\" and \"normalize\" output values
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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 strraw.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); strraw.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 <- backgroundCorrectraw.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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@benilton-carvalho-1375
Last seen 14 months ago
Brazil/Campinas/UNICAMP
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 strraw.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); > > strraw.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 <- backgroundCorrectraw.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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]