On Wed, Oct 24, 2012 at 7:28 AM, anna [guest] <guest@bioconductor.org>wrote:

>
> Hello, when I use this (from carcinoma vs normal example), I select only
> the lowest transcript instead of the higest:
> > o <- order(rowSums(y$counts))
>

This orders the rows from lowest to highest.


> > y <- y[o,]
> > d <- duplicated(y$genes$Symbol)
>

This returns TRUE for all duplicates except the first (working from
top-to-bottom).


> > y <- y[!d,]
>

This effectively chooses the first row in the list for each Symbol.  That
will always be the lowest.

Given what I have told you above, make a change to your code (perhaps the
order() function) that will do what you like.  As a general rule, be sure
to read the help pages (beginning-to-end) for each function you use.
 You'll learn a lot from that.

Sean



> > nrow(y)
>
> what is wrong ?
> I am a novice in informatics.
> and I do not know how to save my list of genes (for example after the
> carcinoma vs normaltissue example).
> many thanks,
> Best regards,
> anna
>
>  -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] edgeR_3.0.0  limma_3.14.1
>
> --
> 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
>

	[[alternative HTML version deleted]]

