[BioC] vsn preprocess with oligo package
José LÓPEZ
jose.lopez at umh.es
Fri Jan 11 16:31:42 CET 2013
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?
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 at 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]]
>>
>>
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
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