Dear Wolfgang,

Thank you very much for your crack-open!! I will try to proceed with these
examples, ASAP.
Just an additional question, I notice that the result object of
'genefilter' function is the logical object (TRUE, FALSE).
It seems like I have to perform one-way ANOVA by myself...Do I mistake
anything?

Thank you very much,
Kaj


2014-06-22 15:49 GMT+07:00 Wolfgang Huber <whuber@embl.de>:

> Kaj
>
> this is an R question, code like the following would do the job
>
> x = … a data.frame with columns ‘probeid’ and ‘pvalue’ ...
> s = split( seq_len(nrow(x)), x$probeid)
> uniqueids = sapply( s, function(i) i[which.min(x$pvalue[i])] )
>
> And you can replace what’s inside the ‘which.min(…)’  expression with
> whatever pleases you.
>
> There are plenty of places in vignettes etc. where this type of operation
> is done. One I happen to be aware of right now is inside the function
> ‘myHeatmap’ of the ‘Hiiragi2013’ package.
>
>
> Wolfgang Huber
>
>
>
>
> On 22 Jun 2014, at 10:02, Kaj Chokeshaiusaha [guest] <
> guest@bioconductor.org> wrote:
>
> > Dear R helpers,
> >
> > I'm working with the goat dataset with no available annotation db. For
> this reason, I use the 'genefilter' instead of 'nsFilter' function with
> ANOVA (p<0.05) (available in 'genefilter' package). The problem is that I
> have the filtered data with 500 ducplicated probes of which I want to
> remove.
> >
> > Due to my limited ability, I cannot figure out how to do them. It would
> be great if I can either select a probe of each duplicates with lowest
> p-value or most variance.
> >
> > Would you please help me with some examples?
> >
> > Best Regards,
> > Kaj
> >
> > -- output of sessionInfo():
> >
> > R version 3.1.0 (2014-04-10)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> > [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> > [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> > [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
> > [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
> > [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods
> > [8] base
> >
> > other attached packages:
> > [1] Biobase_2.24.0      BiocGenerics_0.10.0 genefilter_1.46.1
> >
> > loaded via a namespace (and not attached):
> > [1] annotate_1.42.0      AnnotationDbi_1.26.0 DBI_0.2-7
> > [4] GenomeInfoDb_1.0.2   IRanges_1.22.9       RSQLite_0.11.4
> > [7] splines_3.1.0        stats4_3.1.0         survival_2.37-7
> > [10] tcltk_3.1.0          tools_3.1.0          XML_3.98-1.1
> > [13] xtable_1.7-3
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
> > _______________________________________________
> > 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
>
>

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