[BioC] limma data frame subsetting problem

[axel.klenk at actelion.com]

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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