[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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