[BioC] Sorting matrix by column

Tue Oct 23 17:45:36 CEST 2012

Hi Alex,

Please see the output below:

> str(x)

List of 80
 $ : chr "10371400"
 $ : chr "10453900"
 $ : chr "10375051"
 $ : chr "10575211"
 $ : chr "10566254"
 $ : chr "10602372"
 $ : chr "10398428"
 $ : chr "10383518"
 $ : chr "10397054"
 $ : chr "10384020"
 $ : chr "10608710"
 $ : chr "10363762"
 $ : chr "10375058"
 $ : chr "10381603"
 $ : chr "10442373"
 $ : chr "10421227"
 $ : chr "10534966"
 $ : chr "10398408"
 $ : chr "10398418"
 $ : chr "10572772"
 $ : chr "Lypla1"
 $ : chr "Tcea1"
 $ : chr "Atp6v1h"
 $ : chr "Oprk1"

> class(x[,2])
[1] "list"

On 10/23/12 11:42AM, "Axel Klenk" <axel.klenk at actelion.com> wrote:

>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
>
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>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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>
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