[BioC] Problem with RMA using pdInfoBuilder, oligo and limma
Marc Carlson
mcarlson at fhcrc.org
Wed Jan 28 23:58:53 CET 2009
Hi Anne-Marie,
Is this what you were looking for?:
http://www.bioconductor.org/packages/2.4/data/annotation/html/pd.ragene.1.0.st.v1.html
Marc
Anne-Marie Madore wrote:
> Hi,
>
>
> I am a Ph.D. student from Quebec, Canada. I'm a beginner with R and
> Bioconductor. Until now the only experience I have is in analyzing
> microarray data using affy and limma packages. Now I'm trying to analyze
> Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth
> moderated t test on those arrays. Since no cdf official package is
> available for those arrays, after reading many of the questions and
> responses on this mailing list, I decided to use pdInfoBuilder, oligo
> and limma packages to run analysis.
>
> I built my package according to info available at this web site:
> http://article.gmane.org/gmane.science.biology.informatics.conductor/189
> 63/match=oligo+s
> Below is the output of the installation.
>
> The problem is, after running RMA and moderated T-test, I get expression
> and differential expression measured for all probe separately but not
> the calculated expression for all probes representing a gene. When I run
> RMA, I got only two steps, Background correcting and Normalizing but not
> Calculating expression. Do you know how I can get differential
> expression calculated for each gene? I don't know if the problem is in
> the package I built or if I can use some code to answer this question.
> Below I list warning messages I have when I check my package after
> installation with R CMD check and codes used to analyze expression
> arrays.
>
> Many thanks for your help,
>
> Anne-Marie Madore
> Universite Laval/UQAC
>
>
> ## installing the package in cmd command shell
>
> c:\Program Files\R\R-2.8.1\bin>R CMD INSTALL pd.ragene.1.0.st.v1
> installing to 'c:/PROGRA~1/R/R-28~1.1/library'
>
>
> ---------- Making package pd.ragene.1.0.st.v1 ------------
> adding build stamp to DESCRIPTION
> installing NAMESPACE file and metadata
> installing R files
> installing inst files
> preparing package pd.ragene.1.0.st.v1 for lazy loading
> Loading required package: RSQLite
> Loading required package: DBI
> Loading required package: oligoClasses
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> no man files in this package
> installing indices
> installing help
> adding MD5 sums
>
> * DONE (pd.ragene.1.0.st.v1)
>
>
>
> ## If I run a check (R CMD check pd.ragene.st.v1) I get three warning
> messages and one note:
>
> 1. * checking R files for non-ASCII characters ... WARNING
> Found the following files with non-ASCII characters: all.R Portable
> packages must use only ASCII characters in their R code, except perhaps
> in comments.
>
> 2. * checking whether the name space can be loaded with stated
> dependencies ... WARNING
> Error in initDbConnection() : could not find function "dbConnect" Error:
> .onLoad failed in 'loadNamespace' for 'pd.ragene.1.0.st.v1' Execution
> halted A namespace must be able to be loaded with just the base
> namespace loaded:
> otherwise if the namespace gets loaded by a saved object, the session
> will be unable to start.
> Probably some imports need to be declared in the NAMESPACE file.
>
> 3. * checking R code for possible problems ... NOTE
> closeDb: no visible binding for global variable 'dbCon'
>
> 4. * checking for missing documentation entries ... WARNING
> Undocumented code objects:
> pd.ragene.1.0.st.v1
> All user-level objects in a package should have documentation entries.
> See the chapter 'Writing R documentation files' in manual 'Writing R
> Extensions'.
>
>
> ## analyzing the package
>
>
>> library(Biobase)
>>
> Loading required package: tools
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>
>> library(pdInfoBuilder)
>>
> Loading required package: RSQLite
> Loading required package: DBI
> Loading required package: affxparser
> Loading required package: oligo
> Loading required package: splines
> Loading required package: preprocessCore
> Loading required package: AnnotationDbi
> Loading required package: oligoClasses
> oligo Package - Series 1.5.x
>
>> setwd("D:/Anne-Marie/Doctorat/puces ADN macrophages/puces rat/Annie
>>
> Dube/Analyse")
>
>> library("pd.ragene.1.0.st.v1")
>> library(oligo)
>> library(limma)
>> library(genefilter)
>>
> Loading required package: survival
>
>> library(geneplotter)
>>
> Loading required package: lattice
> Loading required package: annotate
> Loading required package: xtable
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
>
>> cel.files <- list.celfiles(".", full.names = TRUE)
>> basename(cel.files)
>>
> [1] "AD_Ctrl_1.CEL" "AD_Ctrl_2.CEL" "AD_Ctrl_3.CEL"
> "AD_Ctrl_5.CEL"
> [5] "AD_Ctrl_6.CEL" "AD_Traite_10.CEL" "AD_Traite_11.CEL"
> "AD_Traite_7.CEL"
> [9] "AD_Traite_8.CEL" "AD_Traite_9.CEL"
>
>> test <- read.celfiles(cel.files)
>>
> Platform design info loaded.
>
>> phenoData(test) <- read.AnnotatedDataFrame("phenoData.txt", header =
>>
> TRUE, row.name=1)
>
>> class(test)
>>
> [1] "GeneFeatureSet"
> attr(,"package")
> [1] "oligoClasses"
>
>> class(phenoData)
>>
> [1] "standardGeneric"
> attr(,"package")
> [1] "methods"
>
>> eset <- rma(test)
>>
> Background correcting
> Normalizing
>
>> e <- exprs(eset)
>> design <- model.matrix(~factor(eset$Key))
>> fit <- lmFit(eset, design)
>> ebayes <- eBayes(fit)
>>
>>
>>
> ## also a try with slightly the same method as used to make the link
> between phenol data and .CEL with affy package
>
>
>> pd <- read.AnnotatedDataFrame("pheno.txt", header = TRUE, row.names =
>>
> 1)
>
>> pData(pd)
>>
> Phenotype
> AD_Ctrl_1.CEL Control
> AD_Ctrl_2.CEL Control
> AD_Ctrl_3.CEL Control
> AD_Ctrl_5.CEL Control
> AD_Ctrl_6.CEL Control
> AD_Traite_7.CEL Traited
> AD_Traite_8.CEL Traited
> AD_Traite_9.CEL Traited
> AD_Traite_10.CEL Traited
> AD_Traite_11.CEL Traited
>
>> a <- read.celfiles(filenames = rownames(pData(pd)), phenoData = pd,
>>
> verbose = TRUE)
> Platform design info loaded.
>
>> eset <- rma(a)
>>
> Background correcting
> Normalizing
>
>> exprs.eset <- exprs(eset)
>> population.groups <- factor (c(rep("Control",5), rep ("Traited",5)))
>> design <- model.matrix (~population.groups)
>> fit <- lmFit (eset, design)
>> fit.eBayes <- eBayes (fit)
>>
>> sessionInfo()
>>
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines tools stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4
>
> [4] lattice_0.17-17 genefilter_1.22.0 survival_2.34-1
>
> [7] limma_2.16.3 pd.ragene.1.0.st.v1_0.0.1
> pdInfoBuilder_1.6.0
> [10] oligo_1.6.0 oligoClasses_1.4.0
> AnnotationDbi_1.4.2
> [13] preprocessCore_1.4.0 affxparser_1.14.2 RSQLite_0.7-1
>
> [16] DBI_0.2-4 Biobase_2.2.1
>
> loaded via a namespace (and not attached):
> [1] grid_2.8.1 KernSmooth_2.22-22 RColorBrewer_1.0-2
>
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