[BioC] affycoretools repost

James W. MacDonald jmacdon at med.umich.edu
Tue Jun 24 16:17:34 CEST 2008 

Hi Louisa,

Louisa A Rispoli/AS/EXP/UTIA wrote:
> Hi all-
> 
> I am fairly new to bioconductor and am very excited about the example
> described in the affycoretools vignette since 1) it would make my mentor
> very happy (almost the exact situation that we have in the data set), 2)
> seemed like a simple solution to a issue I was not sure how to approach and
> 3) package seemed straightforward and easy to use.  This is probably a
> stupid question arising from the fact that I have yet to fully understand R
> and bioconductor but I have tried to spend a better portion of the day
> trying to figure where I am going wrong and having no luck. I am trying to
> compare samples (two treatment groups)  amplified two different ways and
> see which differentially expressed genes are shared between the two
> different methodologies. According to the PCA plot I need to compute the
> expression values for each methodology separately and then combine the
> data. I can not seem to create the new expression set properly to perform
> the limma analysis.   I have attached a text file with my R code.
> 
>  If anyone could point me in the right direction (either the mistake I am
> makeing or even the vignette that I should read closer) I would appreciate
> the help. Sorry if this seems very silly but we do not have anyone here
> familiar with Bioconductor to go to for help.
> 
> Thanks
> 
> Louisa
> 
> Sorry required a repost, forgot that attachments were stripped.
> 
> R version 2.7.0 (2008-04-22)
> Copyright (C) 2008 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>> library(affycoretools)
> Loading required package: affy
> 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)'.
> 
> Loading required package: affyio
> Loading required package: preprocessCore
> Loading required package: limma
> Loading required package: GOstats
> Loading required package: graph
> Loading required package: GO.db
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Loading required package: RSQLite
> Loading required package: annotate
> Loading required package: xtable
> Loading required package: RBGL
> Loading required package: Category
> Loading required package: genefilter
> Loading required package: survival
> Loading required package: splines
> Loading required package: biomaRt
> Loading required package: RCurl
> 
> Attaching package: 'biomaRt'
> 
> 
>         The following object(s) are masked from package:annotate :
> 
>          getGO
> 
> Loading required package: gcrma
> Loading required package: matchprobes
> Loading required package: annaffy
> Loading required package: KEGG.db
> 
> Attaching package: 'annaffy'
> 
> 
>         The following object(s) are masked from package:RCurl :
> 
>          getURL
> 
> Warning messages:
> 1: package 'DBI' was built under R version 2.7.1
> 2: package 'RSQLite' was built under R version 2.7.1
> 3: package 'xtable' was built under R version 2.7.1
> 
>> pd <-read.AnnotatedDataFrame("pData.txt", sep="\t", header=TRUE,
> row.names=1)
>> dat <- ReadAffy(phenoData= pd)
>> pData(dat)
>                amp  trt
> PolyC-1.CEL  PolyA Ctrl
> PolyC-2.CEL  PolyA Ctrl
> PolyC-3.CEL  PolyA Ctrl
> PolyC-4.CEL  PolyA Ctrl
> PolyC-5.CEL  PolyA Ctrl
> PolyC-6.CEL  PolyA Ctrl
> PolyC-7.CEL  PolyA Ctrl
> PolyC-8.CEL  PolyA Ctrl
> PolyHS-1.CEL PolyA   HS
> PolyHS-2.CEL PolyA   HS
> PolyHS-3.CEL PolyA   HS
> PolyHS-4.CEL PolyA   HS
> PolyHS-5.CEL PolyA   HS
> PolyHS-6.CEL PolyA   HS
> PolyHS-7.CEL PolyA   HS
> PolyHS-8.CEL PolyA   HS
> WTC-1.CEL       WT Ctrl
> WTC-2.CEL       WT Ctrl
> WTC-3.CEL       WT Ctrl
> WTC-4.CEL       WT Ctrl
> WTC-5.CEL       WT Ctrl
> WTC-6.CEL       WT Ctrl
> WTC-7.CEL       WT Ctrl
> WTC-8.CEL       WT Ctrl
> WTHS-1.CEL      WT   HS
> WTHS-2.CEL      WT   HS
> WTHS-3.CEL      WT   HS
> WTHS-4.CEL      WT   HS
> WTHS-5.CEL      WT   HS
> WTHS-6.CEL      WT   HS
> WTHS-7.CEL      WT   HS
> WTHS-8.CEL      WT   HS
> 
>> eset <-affystart(groups=rep(1:4, each = 8), groupsnames =
> unique(paste(pData(pd)[,1],pData(pd)[,2], sep="-")), phenoData = pd)
> Background correcting
> Normalizing
> Calculating Expression
> 
>> eset1 <-affystart(filenames=list.celfiles()[1:16], plot = FALSE,
> pca=FALSE)
> Background correcting
> Normalizing
> Calculating Expression
> 
>> eset2 <-affystart(filenames=list.celfiles()[17:32], plot=FALSE,
> pca=FALSE)
> Background correcting
> Normalizing
> Calculating Expression
> 
>> eset <- new("ExpressionSet", exprs=cbind(exprs(eset1), exprs(eset2)),
> phenoData = pd, annotation=annotation(eset1))
> Error in validObject(.Object) :
>   invalid class "ExpressionSet" object: sampleNames differ between
> assayData and phenoData

That's odd. What do you get for sampleNames(pd)?


> 
>> eset1
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 24128 features, 16 samples
>   element names: exprs
> phenoData
>   sampleNames: PolyC-1.CEL, PolyC-2.CEL, ..., PolyHS-8.CEL  (16 total)
>   varLabels and varMetadata description:
>     sample: arbitrary numbering
> featureData
>   featureNames: AFFX-BioB-3_at, AFFX-BioB-5_at, ..., BtAffx.29968.1.S1_at
> (24128 total)
>   fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation: bovine
> 
>> eset2
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 24128 features, 16 samples
>   element names: exprs
> phenoData
>   sampleNames: WTC-1.CEL, WTC-2.CEL, ..., WTHS-8.CEL  (16 total)
>   varLabels and varMetadata description:
>     sample: arbitrary numbering
> featureData
>   featureNames: AFFX-BioB-3_at, AFFX-BioB-5_at, ..., BtAffx.29968.1.S1_at
> (24128 total)
>   fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation: bovine
> 
> "If we knew what we were doing, it wouldn't be called Research." - Albert
> Einstein
> 
> Louisa Rispoli, Ph.D. Reproductive Physiology
> Department of Animal Science
> University of Tennessee, Knoxville
> A105 Johnson Animal Research and Teaching Unit
> 1750 Alcoa Highway
> Knoxville, TN 37920
> phone:(865) 946-1874
> fax:(865) 946-1010
> email: lrispoli at utk.edu
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> 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
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

More information about the Bioconductor mailing list