[BioC] vsn preprocess with oligo package

James W. MacDonald jmacdon at uw.edu
Fri Jan 11 15:59:43 CET 2013


Hi Jose,

Let's say you followed Benilton's code from 
https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html

library(oligo)
cels = list.celfiles()
raw = read.celfiles(cels)
raw = backgroundCorrect(raw, "rma") ## I added this - you might want BG 
correction
pms = pm(raw)
pmsVSN = vsn::vsnMatrix(pms)
pm(raw) <- pmVSN
rm(pms, pmsVSN)

you now have an ExpressionFeatureSet with normalized data that you want 
to summarize. You can then

eset <- summarize(raw, method = "medianpolish")

See

?summarizationMethods

for more information.

Best,

Jim


On 1/11/2013 6:17 AM, José LÓPEZ wrote:
> Dear Benilton,
>
> I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, I would also like to pre-process with vsn. I have seen previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html), but unfortunately, I am not bioinformatician and, although I read oligo and vsn manuals, it is not easy to me to follow up to summarize the vsn object.
> May you (or someone else) please, give me some additional clue to sumarize the vsn object using the oligo package.
>
> Thank you very much in advance for your time and your kind help,
>
>   Jose LOPEZ
>
> **************************
>
>> list.files()
> [1] "ABRNA1.CEL"                          "ABRNA2.CEL"                          "ABRNA3.CEL"
> [4] "ABRNA4.CEL"                          "ABRNA5.CEL"                          "ABRNA6.CEL"
> [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R"
>> library(limma)
>> library(oligo)
> Loading required package: BiocGenerics
>
> Attaching package: ‘BiocGenerics’
>
> The following object(s) are masked from ‘package:stats’:
>
>      xtabs
>
> The following object(s) are masked from ‘package:base’:
>
>      anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply,
>      mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply,
>      setdiff, table, tapply, union, unique
>
> Loading required package: oligoClasses
> Loading package bit 1.1-9
> package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
> creators: bit bitwhich
> coercion: as.logical as.integer as.bit as.bitwhich which
> operator: !&  | xor != ==
> querying: print length any all min max range sum summary
> bit access: length<- [ [<- [[ [[<-
> for more help type ?bit
> Loading package ff2.2-10
> - getOption("fftempdir")=="/var/folders/U+/U+SFMmqcEbKkSysJQ3OYbk+++TQ/-Tmp-//RtmpKgQzWD"
>
> - getOption("ffextension")=="ff"
>
> - getOption("ffdrop")==TRUE
>
> - getOption("fffinonexit")==TRUE
>
> - getOption("ffpagesize")==65536
>
> - getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes
>
> - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
>
> - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
>
> Welcome to oligoClasses version 1.20.0
> Loading required package: Biobase
> Welcome to Bioconductor
>
>      Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
>      'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> ========================================================================================================================
> Welcome to oligo version 1.22.0
> ========================================================================================================================
>
> Attaching package: ‘oligo’
>
> The following object(s) are masked from ‘package:limma’:
>
>      backgroundCorrect
>
>> Data=read.celfiles(list.celfiles())
> Loading required package: pd.mogene.1.0.st.v1
> Loading required package: RSQLite
> Loading required package: DBI
> Platform design info loaded.
> Reading in : ABRNA1.CEL
> Reading in : ABRNA2.CEL
> Reading in : ABRNA3.CEL
> Reading in : ABRNA4.CEL
> Reading in : ABRNA5.CEL
> Reading in : ABRNA6.CEL
>> pms=pm(Data)
>> class(pms)
> [1] "matrix"
>> head(pms)
>       ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL
> 2106         46         43         36         36         37         33
> 2107         38         32         33         36         43         34
> 2108         31         31         35         34         37         35
> 2109         54         46         45         40         58         35
> 2110         58         55         40         39         94         40
> 2111         53         39         34         36         43         43
>> pmsVSN=vsn::vsnMatrix(pms)
> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit.
>> class(pmsVSN)
> [1] "vsn"
> attr(,"package")
> [1] "vsn"
>> pmsVSN
> vsn object for n=899636 features and d=6 samples.
> sigsq=0.026
> hx: 899636 x 6 matrix.
>> eset=rma(pmsVSN, background=FALSE,normalize=FALSE)
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function ‘rma’ for signature ‘"vsn"’
>
>> library(vsn)
>> meanSdPlot(pmsVSN)
> KernSmooth 2.23 loaded
> Copyright M. P. Wand 1997-2009
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] vsn_3.26.0                pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2            DBI_0.2-5
> [5] oligo_1.22.0              Biobase_2.18.0            oligoClasses_1.20.0       BiocGenerics_0.4.0
> [9] limma_3.14.3
>
> loaded via a namespace (and not attached):
>   [1] affxparser_1.30.0     affy_1.36.0           affyio_1.26.0         BiocInstaller_1.8.3   Biostrings_2.26.2
>   [6] bit_1.1-9             codetools_0.2-8       ff_2.2-10             foreach_1.4.0         GenomicRanges_1.10.5
> [11] grid_2.15.2           IRanges_1.16.4        iterators_1.0.6       KernSmooth_2.23-8     lattice_0.20-10
> [16] parallel_2.15.2       preprocessCore_1.20.0 splines_2.15.2        stats4_2.15.2         tools_2.15.2
> [21] zlibbioc_1.4.0
>
>
> 	[[alternative HTML version deleted]]
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099



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