[BioC] remove.dupEntrez from nsFilter{genefilter}

[James W. MacDonald]

Hi Klemens,

On 5/29/2012 1:45 PM, Klemens Vierlinger [guest] wrote:
> Dear List,
> I seem to have a problem with the nsFilter function. For genes which are represented by more than one probe, it should keep the probe with the highest IQR and delete the others. It seems to me that in the example below this is not the case.
>
> Any ideas why?

It has to do with how the IQR is calculated.

 > x <- genefilter:::rowIQRs(exprs(test.es))
 > names(x) <- featureNames(test.es)
 > y <- apply(exprs(test.es), 1, IQR)
 > names(y) <- featureNames(test.es)
 > z <- get("AKT3", revmap(HsAgilentDesign026652SYMBOL))
 > data.frame(x[z], y[z], row.names = z)
                  x.z.     y.z.
A_23_P160354 2.162743 2.096952
A_24_P110983 2.177948 2.071818

So as far as genefilter is concerned, A_24_P110983 has a higher IQR.

Best,

Jim


>
> Best
> Klemens
>
>
>
> require(genefilter)
> con<- url('http://rdf.ait.ac.at/attachments/download/102/test.es')
> load(con)
> close(con)
>
> # the expressionset test.es contains two probes for the ACT3 genes, where A_23_P160354 is the one with the highest IQR.
> exprs(test.es)[fData(test.es)$ENTREZ %in% 10000, ]
> apply(exprs(test.es)[fData(test.es)$ENTREZ %in% 10000, ], 1, IQR)
>
> #However, if I apply nsFilter, the other Probe is kept
> remDup<- nsFilter(test.es, var.filter=F)$eset
> featureNames(remDup)[fData(remDup)$ENTREZ %in% 10000]
> exprs(remDup)[fData(remDup)$ENTREZ %in% 10000]
>
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.13.2 (2011-09-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] HsAgilentDesign026652.db_2.5.0 org.Hs.eg.db_2.5.0             RSQLite_0.10.0                 DBI_0.2-5
> [5] AnnotationDbi_1.16.11          genefilter_1.34.0              Biobase_2.12.2
>
> loaded via a namespace (and not attached):
> [1] annotate_1.30.1 IRanges_1.10.6  splines_2.13.2  survival_2.36-9 tools_2.13.2    xtable_1.6-0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at 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