[BioC] nsfilter error from expressionset obtained after using aroma for processing

[Wolfgang Huber]

Dear Andreia

do you need the 'nsFilter' filter function for this purpose (which is great but perhaps a bit over-engineered) or would you already be helped by doing this using basic R functionality, e.g. 

        m = rowMeans(exprs(eset))
        esetf = eset[ m> quantile(m, probs=theta), ]

Please also note the new vignette on filtering, http://www.bioconductor.org/packages/devel/bioc/html/genefilter.html --> Diagnostics for independent filtering.

	Hope this helps
	Wolfgang
  


El Apr 1, 2013, a las 4:32 pm, Andreia Fonseca <andreia.fonseca at gmail.com> escribió:

> Dear all,
> 
> 
> I am analyzing data obtained using the HuGene2.0-st arrays from affymetrix.
> 
> I have used aroma for preprocessing and limma for diff. expression
> analysis. After multiple testing I lost significance and therefore I want
> to filter out genes that do not have a potential to be significantly
> different.
> 
> So I have created an expression set after rma
> 
> 
> plm <- RmaPlm(csN)
> 
> fit(plm, verbose=verbose)
> 
> ces <- getChipEffectSet(plm)
> 
> eset <- extractExpressionSet(ces)
> 
> ans <- nsFilter(eset)
> 
> I am getting an error at this point:
> 
> Error in if (nchar(annChip) == 0) stop("'eset' must have a valid annotation
> slot") :
>  argument is of length zero
> 
> .
> 
> I understand that is because the annotation field is empty. But how can I
> overcome this?
> 
> Thanks Andreia
> 
> the ces object
> 
> ChipEffectSet:
> Name: Jurkat_0_vs_over_2
> Tags: RBC,QN,RMA
> Path:
> Documents/analysis_affy_arrays/plmData/Jurkat_0_vs_over_2,RBC,QN,RMA/HuGene-2_0-st
> Platform: Affymetrix
> Chip type: HuGene-2_0-st,r3_binary,monocell
> Number of arrays: 6
> Names: Ju_0_1_1, Ju_0_2_2, Ju_0_3_3, ..., Ju_34c_5_6 [6]
> Time period: 2013-03-27 16:56:07 -- 2013-03-27 16:56:08
> Total file size: 3.08MB
> RAM: 0.01MB
> Parameters: {}
> 
> the eset object:
> 
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 53617 features, 6 samples
>  element names: exprs
> protocolData: none
> phenoData: none
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation:
> 
> 
> sessionInfo()
> 
> R version 2.15.3 (2013-03-01)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
> 
> other attached packages:
> [1] hgu95av2.db_2.8.0      org.Hs.eg.db_2.8.0     RSQLite_0.11.2
> DBI_0.2-5              AnnotationDbi_1.20.7   BiocInstaller_1.8.3
> genefilter_1.40.0
> [8] GenomeGraphs_1.18.0    biomaRt_2.14.0         limma_3.14.4
> gplots_2.11.0          MASS_7.3-23            KernSmooth_2.23-10
> caTools_1.14
> [15] gdata_2.12.0           gtools_2.7.1           Biobase_2.18.0
> BiocGenerics_0.4.0     aroma.affymetrix_2.8.0 affxparser_1.30.2
> aroma.apd_0.2.3
> [22] R.huge_0.4.1           aroma.light_1.28.0     aroma.core_2.8.3
> matrixStats_0.6.2      R.rsp_0.8.2            R.devices_2.1.3
> R.cache_0.6.5
> [29] R.filesets_2.0.0       R.utils_1.23.2         R.oo_1.13.0
> affy_1.36.1            R.methodsS3_1.4.2
> 
> loaded via a namespace (and not attached):
> [1] IRanges_1.16.6        PSCBS_0.30.0          RCurl_1.95-4.1
> XML_3.96-1.1          affyio_1.26.0         annotate_1.36.0
> bitops_1.0-4.2
> [8] digest_0.6.3          parallel_2.15.3       preprocessCore_1.20.0
> splines_2.15.3        stats4_2.15.3         survival_2.37-4
> tools_2.15.3
> [15] xtable_1.7-1          zlibbioc_1.4.0
> 
> 
> 
> 
> 
> ---------------------------------------------------------------------------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral at fm.ul.pt ; andreiaamaral at fc.ul.pt
> 
> 	[[alternative HTML version deleted]]
> 
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