[BioC] limma data frame subsetting problem

[axel.klenk at actelion.com]

No, I meant rowMax() from package Biobase but obviously this functionality
has been implemented several times... rowMaxs() from fBasics (if that's 
the
one you've found) is less efficient but it will hardly make a difference 
for your
use case - as in fortune(98)... :-)

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
Jabez Wilson <jabezwuk at yahoo.co.uk>
To:
axel.klenk at actelion.com
Cc:
bioconductor at r-project.org, bioconductor-bounces at r-project.org
Date:
05.10.2011 16:22
Subject:
Re: [BioC] limma data frame subsetting problem




Yes, thanks, Axel, I think that may well do the trick - assuming you meant 
rowMaxs() ;-)
 
You're right, it is an RGList not a DF.
 
Jab
 

--- On Wed, 5/10/11, axel.klenk at actelion.com <axel.klenk at actelion.com> 
wrote:

From: axel.klenk at actelion.com <axel.klenk at actelion.com>
Subject: Re: [BioC] limma data frame subsetting problem
To: "Jabez Wilson" <jabezwuk at yahoo.co.uk>
Cc: bioconductor at r-project.org, bioconductor-bounces at r-project.org
Date: Wednesday, 5 October, 2011, 10:42

Dear Jabez, 

try:

RG[rowMax(RG$G) > 5000, ]

Is that what you want? 

And BTW, note that you are dealing with an RGList and not a data frame...

Cheers,

- axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
Jabez Wilson <jabezwuk at yahoo.co.uk>
To:
bioconductor at r-project.org
Date:
05.10.2011 11:15
Subject:
[BioC] limma data frame subsetting problem
Sent by:
bioconductor-bounces at r-project.org








Dear Bioconductors, I want to do something simple, which I cannot find the 

solution to. I have a limma data frame and I want to select a subset of 
the data frame based on whether the values in the "G" channel are > e.g. 
5000
As an example I use swirl data
targets <- readTargets("SwirlSample.txt"); RG <- read.maimages(targets, 
source="spot")
> head(RG$G)
       swirl.1   swirl.2    swirl.3    swirl.4
[1,] 22028.260 19278.770  2727.5600 19930.6500
[2,] 25613.200 21438.960  2787.0330 25426.5800
[3,] 22652.390 20386.470  2419.8810 16225.9500
[4,]  8929.286  6677.619   383.2381   786.9048
[5,]  8746.476  6576.292   901.0000   468.0476
[6,] 37010.080 23769.100 23377.9700 28399.0900


I can select the first 20 lines of the df by 
>RG[1:20,]
but I really want to select those lines of the df (and keep the df format 
intact) where the "G" value in any column is > a certain figure (e.g. 
5000)
However, 
> RG[RG$G>5000,]
Error in `[.RGList`(RG, RG$G > 5000, ) : 
  (subscript) logical subscript too long

I have no success with subset either:
> subset(RG, RG$G>5000,)
Error: Two subscripts required
> subset(RG$G, RG$G>5000)
Error in subset.matrix(RG$G, RG$G > 5000) : 
  (subscript) logical subscript too long


Do I need to write a loop to check each column of "G" seperately? Or is 
there a simpler solution?
TIA
Jabez

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