[BioC] Sorting matrix by column

[Axel Klenk]

Dear Guest,

I think your approach is valid in general and it is your x that is causing the
problem; column 'Gene Symbol' appears to contain two values. What is the
result of

str(x)

and/or

class(x[,2])

?

Cheers,

 - axel


Axel Klenk
Research Informatician
Information Management Drug Discovery

Actelion Pharmaceuticals Ltd. • Gewerbestrasse 16 • CH-4123 Allschwil
• Switzerland
G12.O1.R10

axel.klenk at actelion.com • www.actelion.com
Address for visitors: Hegenheimermattweg 92



On Tue, Oct 23, 2012 at 5:15 PM, Guest [guest] <guest at bioconductor.org> wrote:
>
>
> Hi,
>
> I would like to sort a matrix by a specific column (column 2). I tried the order() function, but I get an error. I think it is because the values in column 2 are not numeric, they are gene symbols. This may be a general R question, but I thought I would post it here since it is microarray data analysis.
>
> I have matrix x:
>
> > x
>          ID         Gene Symbol     logFC      Adj.PVal
> 10344624 "10371400" "Lypla1"        0.3592492  0.9999522
> 10344633 "10453900" "Tcea1"         0.1886117  0.9999522
> 10344637 "10375051" "Atp6v1h"       0.6713107  0.9999522
> 10344653 "10575211" "Oprk1"         -0.2342731 0.9999522
> 10344658 "10566254" "Rb1cc1"        1.790676   0.9999522
> 10344674 "10602372" "Fam150a"       1.397496   0.9999522
> 10344679 "10398428" "St18"          -0.3278807 0.9999522
> 10344707 "10383518" "Pcmtd1"        -0.2231074 0.9999522
> 10344713 "10397054" "Ahcy"          -0.1844897 0.9999522
> 10344723 "10384020" "Rrs1"          -0.2322781 0.9999522
> 10344725 "10608710" "Adhfe1"        0.5993566  0.9999522
> 10344741 "10363762" "Hnrnpa3"       -0.2660978 0.9999522
> 10344743 "10375058" "3110035E14Rik" 0.9178868  0.9999522
> 10344750 "10381603" "Sgk3"          -0.2961638 0.9999522
> 10344772 "10442373" "6030422M02Rik" -0.1653454 0.9999522
> 10344789 "10421227" "Cspp1"         -0.1480766 0.9999522
> 10344799 "10534966" "Cspp1"         -0.2436361 0.9999522
> 10344801 "10398408" "Cspp1"         -0.4040665 0.9999522
> 10344803 "10398418" "Cspp1"         -0.2556627 0.9999522
> 10344805 "10572772" "Cspp1"         -0.1864641 0.9999522
>
> I want to sort on the "Gene Symbol" column so that I can remove the duplicates and keep the one with the highest log fold change.
>
> I tried the following and received an error.
> > x[order(x[,2]),]
> Error in order(x[, 2]) : unimplemented type 'list' in 'orderVector1'
>
> If anyone has any suggestions for an easy way to sort a significant gene list, remove duplicated values, and keep the value with highest fold change, that would be helpful!
>
> I've posted my session info below.
>
> Thanks!
>
> Guest
>
>  -- output of sessionInfo():
>
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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