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       


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