[BioC] Sorting matrix by column
Kasoji, Manjula (NIH/NCI) [C]
manjula.kasoji at nih.gov
Tue Oct 23 20:32:25 CEST 2012
Thanks, guys. I think I got that because I did a cbind() with my ebayes()
results and my annotation results from mget() that used to annotate my
significant genes from the mogene10sttranscriptcluster db.
I'll try out a few things. If you guys have any further suggestions or
recommendations I will certainly appreciate them.
Thanks!
On 10/23/12 11:57AM, "Axel Klenk" <axel.klenk at actelion.com> wrote:
>Dear Manjula,
>
>wow. How did you create that? :-)
>
>order() doesn't like lists:
>
>> order(list(1:3))
>Error in order(list(1:3)) : unimplemented type 'list' in 'orderVector1'
>
>and I think you should try to make your x look something like the
>data.frame that Jim has used in his example and it will work.
>
>Cheers,
>
>Axel (not Alex!!) 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 5:45 PM, Kasoji, Manjula (NIH/NCI) [C]
><manjula.kasoji at nih.gov> wrote:
>> 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
>>>
>>>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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>>
>
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