Dear James, 

It worked perfectly, thanks a lot 

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@udc.es 
---------------------------------------------------------------- 



De: "James W. MacDonald" <jmacdon@uw.edu> 
Para: "Juan Fernández Tajes" <jfernandezt@udc.es> 
CC: Bioconductor@r-project.org 
Enviados: Martes, 8 de Mayo 2012 18:32:43 
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 11:14 AM, Juan Fernández Tajes wrote: 
> Sorry for take our first conversation off-list, I just forgot to click 
> reply all. I already changed the annotation slot to: 
> annotation(myAB1_rma) <- "hugene11sttranscriptcluster.db", as you has 
> suggested. However, when I execute the nsFilter command: 
> 
> >filt_myAB1 = nsFilter(myAB1_rma,var.func=IQR, 
> var.cutoff=0.5,feature.exclude=IDs) 
> 
> In the filter.log I find this: 
> 
> $filter.log 
> $filter.log$numDupsRemoved 
> [1] 2013 
> 
> $filter.log$numLowVar 
> [1] 9968 
> 
> $filter.log$numRemoved.ENTREZID 
> [1] 11348 
> 
> I don´t find a filter.log$feature.exclude, I´ve also tried converting 
> object IDs to character but it doesn´t work neither 

OK, but what do you get when you do 

sum(as.character(IDs) %in% featureNames(filt_myAB1$eset)) 

if it is 0, then you have filtered them all out. 

Best, 

Jim 


> 
> Thanks a lot 
> 
> 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@udc.es 
> ---------------------------------------------------------------- 
> 
> 
> ------------------------------------------------------------------------
> *De: *"James W. MacDonald" <jmacdon@uw.edu> 
> *Para: *"Juan Fernández Tajes" <jfernandezt@udc.es> 
> *CC: *Bioconductor@r-project.org 
> *Enviados: *Martes, 8 de Mayo 2012 17:04:49 
> *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, 
> 
> 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@udc.es 
> > ---------------------------------------------------------------- 
> > 
> > 
> > ------------------------------------------------------------------------ 
> > *De: *"James W. MacDonald" <jmacdon@uw.edu> 
> > *Para: *"Juan Fernández Tajes" <jfernandezt@udc.es> 
> > *CC: *bioconductor@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 bioconductorÂ´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 doesnÂ´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 CoruÃ±a 
> > > Tlf. +34 981 167000 ext 2030 
> > > e-mail: jfernandezt@udc.es 
> > > ---------------------------------------------------------------- 
> > > 
> > > 
> > > 
> > > [[alternative HTML version deleted]] 
> > > 
> > > 
> > > 
> > > _______________________________________________ 
> > > Bioconductor mailing list 
> > > Bioconductor@r-project.org 
> > > 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 
> > 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 
> 

-- 
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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