[BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray
James W. MacDonald
jmacdon at uw.edu
Tue May 8 17:04:49 CEST 2012
Hi Juan,
Please don't take conversations off-list. We like to think of the
archives as a resource, and if conversations are taken off-list, that
purpose is subverted.
On 5/8/2012 10:30 AM, Juan Fernández Tajes wrote:
> Dear James,
>
> Thanks for your quick answer here is the code that I´ve used and the
> sessionInfo:
>
> >library(pd.hugene.1.1.st.v1)
> >library(genefilter)
> >library(oligo)
> >library(limma)
> >tab <- dbGetQuery(con, "select * from featureSet;")
Note that you could do this more elegantly:
probes.control <- dbGetQuery(con, "select fsetid from featureSet where
type in ('2','4','6','7');")[,1]
> >probes.control <- subset(tab, tab$type=="2" | tab$type=="4" |
> tab$type=="6" | tab$type=="7")
> >IDs <- probes.control$fsetid
> >geneCELs <- list.celfiles("./CEL", full.names=T)
> >affyGeneFS <- read.celfiles(geneCELs)
> >myAB <- affyGeneFS
> >sampleNames(myAB) <- sub("\\.CEL$", "", sampleNames(myAB))
> >metadata_array <- read.delim(file="metadata_array_oligo.txt",
> header=T, sep="\t")
> >rownames(metadata_array) <- metadata_array$Sample_ID
> >phenoData(myAB) <- new("AnnotatedDataFrame", data=metadata_array)
> >myAB1 <- myAB[, -10]
> >myAB1_rma <- rma(myAB1, target="core")
> >filt_myAB1 = nsFilter(myAB1_rma,var.func=IQR,
> var.cutoff=0.5,feature.exclude=IDs)$eset
>
> And here is the error that I find when trying to filter:
> >filt_myAB1 = nsFilter(myAB1_rma,var.func=IQR,
> var.cutoff=0.5,feature.exclude=IDs)$eset
> Error en get(mapName, envir = pkgEnv, inherits = FALSE) :
> object 'pd.hugene.1.1.st.v1_dbconn' not found
That is because nsFilter expects a different annotation package. So you
need to change the annotation slot of your GeneFeatureSet:
annotation(myAB1_rma) <- "hugene11sttranscriptcluster.db"
And you will likely need to do
library(BiocInstaller)
biocLite("hugene11sttranscriptcluster.db")
first.
Best,
Jim
>
> And here is the sessioInfo()
>
> R version 2.14.0 (2011-10-31)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] limma_3.10.3 genefilter_1.36.0
> pd.hugene.1.1.st.v1_3.4.0 oligo_1.18.1 oligoClasses_1.16.0
> [6] Biobase_2.14.0 RSQLite_0.11.1 DBI_0.2-5
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.26.4 affyio_1.22.0 annotate_1.32.3
> AnnotationDbi_1.16.19 Biostrings_2.22.0 bit_1.1-8
> [7] ff_2.2-6 IRanges_1.12.6 preprocessCore_1.16.0
> splines_2.14.0 survival_2.36-14 tools_2.14.0
> [13] xtable_1.7-0 zlibbioc_1.0.1
>
> BW,
>
> Juan
>
>
> ---------------------------------------------------------------
> Juan Fernandez Tajes, ph. D
> Grupo XENOMAR
> Departamento de Biología Celular y Molecular
> Facultad de Ciencias-Universidade da Coruña
> Tlf. +34 981 167000 ext 2030
> e-mail: jfernandezt at udc.es
> ----------------------------------------------------------------
>
>
> ------------------------------------------------------------------------
> *De: *"James W. MacDonald" <jmacdon at uw.edu>
> *Para: *"Juan Fernández Tajes" <jfernandezt at udc.es>
> *CC: *bioconductor at r-project.org
> *Enviados: *Martes, 8 de Mayo 2012 15:25:41
> *Asunto: *Re: [BioC] How can I remove control probesets from the
> expressionset object in gene expression analysis with Affy Human Gene
> 1.0ST microarray
>
> Hi Juan,
>
> On 5/8/2012 6:46 AM, Juan Fernández Tajes wrote:
> > Dear Bioconductor subcribers:
> >
> > First of all, I apologize for using a old-resolved bioconductor´s
> thread:https://stat.ethz.ch/pipermail/bioconductor/2011-June/039993.html
> >
> > " Dear list,> > I am quite new to R as well as to microarray
> analysis.> I am dealing with some gene expression analysis performed
> on Affymetrix Human> Gene 1.0ST microarray.> > So far, I have learnt
> how to filtrate data using genefilter using nsFilter> functions.> >
> Now, I would like to know how to filter out from the expressionset
> object all> the control probesets (~4000) that Affymetrix includes in
> the microarray (for> quality assay, normalization, background
> correction, etc.). However, none of> the aforementioned functions
> worked for me.> > How can I recognize those probesets and remove
> them? I would like to filter> them out before statistical analysis
> with limma package."
> >
> > I have been having the same problem when using oligo to analyze the
> data. It so happens that when I try to filter control probe IDs with
> nsfilter it doesn´t work properly. Do you know anyway to get around
> this problem?
>
> Probably. But you don't give us anything to go on. What code did you
> use? What happened? Define 'doesn't work properly'. What is the output
> from sessionInfo()?
>
> Best,
>
> Jim
>
>
> >
> > Many thanks in advance
> >
> > Juan
> >
> > ---------------------------------------------------------------
> > Juan Fernandez Tajes, ph. D
> > Grupo XENOMAR
> > Departamento de BiologÃa Celular y Molecular
> > Facultad de Ciencias-Universidade da Coruña
> > Tlf. +34 981 167000 ext 2030
> > e-mail: jfernandezt at udc.es
> > ----------------------------------------------------------------
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> >
> >
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>
> --
> 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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