Yes, the exprs() did the job and it is allowing me to combine vsn with oligo and Gene ST arrays.

Thank you again for your kind help,

Best,

 Jose


> library(limma)
> library(oligo)
> 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
> Data
GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 1102500 features, 6 samples 
  element names: exprs 
protocolData
  rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.mogene.1.0.st.v1 
> class(Data)
[1] "GeneFeatureSet"
attr(,"package")
[1] "oligoClasses"
> raw=backgroundCorrect(Data,"rma")
Background correcting... OK
> pms=pm(raw)
> head(pms)
     ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL
2106   7.853059   7.635413   5.221570   5.160448   5.978796   5.767533
2107   5.990083   4.764031   4.659925   5.160448   7.067603   5.903628
2108   4.867173   4.587342   5.023095   4.762256   5.978796   6.045105
2109  10.657556   8.827158   7.679404   6.124607  11.523816   6.045105
2110  12.538396  13.906774   6.147958   5.860049  38.764281   6.843026
2111  10.241785   6.356910   4.836138   5.160448   7.067603   7.405633
> class(pms)
[1] "matrix"
> 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=0.1
hx: 899636 x 6 matrix.
> pm(raw) <- exprs(pmsVSN)
> rm(pms, pmsVSN)
> ls()
[1] "Data" "raw" 
> raw
GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 1102500 features, 6 samples 
  element names: exprs 
protocolData
  rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.mogene.1.0.st.v1 
> eset=rma(raw, background=FALSE,normalize=FALSE)
Calculating Expression
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35556 features, 6 samples 
  element names: exprs 
protocolData
  rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.mogene.1.0.st.v1 

El ene 11, 2013, a las 5:07 p.m., James W. MacDonald escribió:

> Hi Jose,
> 
> On 1/11/2013 10:31 AM, José LÓPEZ wrote:
>> Dear Jim,
>> 
>> Thank you for the advise on the background correction step.
>> I already tryed before the whole Benilton's code but it doesn't work at the following step.
>> 
>>> pm(raw)<- pmVSN
>> Error: object 'pmVSN' not found
>> 
>> May I ask you what this step is doing? Does it replace the pm matrix in the raw ExpressionFeatureSet by the normalized one?
> 
> Exactly. But the 'pm <-'  function expects to be fed a matrix, and the pmsVSN isn't a matrix. Instead, it is a 'vsn' object, which is related to an ExpressionSet object. So you can extract the matrix of normalized data as usual, with exprs():
> 
> pm(raw) <- exprs(pmsVSN)
> 
> and there was another error in my code, as summarize() won't work on a GeneFeatureSet object. Instead, you want to use rma():
> 
> eset <- rma(raw, normalize = FALSE, background = FALSE)
> 
> Best,
> 
> Jim
> 
> 
> 
>> 
>> Thank you in advance for your time and your kind help,
>> 
>> Jose
>> 
>>> library(limma)
>>> library(oligo)
>>> 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)
>>> raw=backgroundCorrect(Data,"rma")
>> Background correcting... OK
>>> pms=pm(raw)
>>> pmsVSN=vsn::vsnMatrix(pms)
>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit.
>>> pm(raw)<- pmVSN
>> Error: object 'pmVSN' not found
>>> pm(raw)<- pmsVSN
>> Error in function (classes, fdef, mtable)  :
>>   unable to find an inherited method for function ‘pm<-’ for signature ‘"GeneFeatureSet", "missing", "missing", "vsn"’
>>> pmsVSN
>> vsn object for n=899636 features and d=6 samples.
>> sigsq=0.1
>> hx: 899636 x 6 matrix.
>>> head(pms)
>>      ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL
>> 2106   7.853059   7.635413   5.221570   5.160448   5.978796   5.767533
>> 2107   5.990083   4.764031   4.659925   5.160448   7.067603   5.903628
>> 2108   4.867173   4.587342   5.023095   4.762256   5.978796   6.045105
>> 2109  10.657556   8.827158   7.679404   6.124607  11.523816   6.045105
>> 2110  12.538396  13.906774   6.147958   5.860049  38.764281   6.843026
>> 2111  10.241785   6.356910   4.836138   5.160448   7.067603   7.405633
>>> class(pms)
>> [1] "matrix"
>>> ls()
>> [1] "Data"   "pms"    "pmsVSN" "raw"
>> 
>>> sessionInfo()
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-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] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2            DBI_0.2-5                 oligo_1.22.0
>> [5] Biobase_2.18.0            oligoClasses_1.20.0       BiocGenerics_0.4.0        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       lattice_0.20-10       parallel_2.15.2
>> [16] preprocessCore_1.20.0 splines_2.15.2        stats4_2.15.2         vsn_3.26.0            zlibbioc_1.4.0
>> 
>> 
>> *****************************************************
>> José P. LÓPEZ-ATAYALA
>> Instituto de Neurociencias
>> CSIC - UMH
>> Avda. D. Santiago Ramón y Cajal, S/N
>> E-03550, Sant Joan d'Alacant
>> Alicante, Spain
>> jose.lopez@umh.es
>> http://in.umh.es/grupos-detalle.aspx?grupo=30
>> (34) 965 919 531
>> 
>> El ene 11, 2013, a las 3:59 p.m., James W. MacDonald escribió:
>> 
>>> 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]]
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>>> -- 
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> University of Washington
>>> Environmental and Occupational Health Sciences
>>> 4225 Roosevelt Way NE, # 100
>>> Seattle WA 98105-6099
>>> 
> 
> -- 
> 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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