[BioC] limma reading wrong column for GPR files

[michael watson (IAH-C)]

As far as I know this is correct for limma - the default is to read the mean of pixels for foreground and the median of pixels for background.  The reason being that the median is less sensitive to outliers, and you are more likely to get those in the background.

You can always use the "columns" argument of read.maimages to change this eg:

RG <- read.maimages(blah, blah, blah, columns = list(Rf = "F635 Mean", Rb = "B635 Mean", Gf = "F532 Mean", Gb = "B532 Mean"))

Mick


-----Original Message-----
From:	bioconductor-bounces at stat.math.ethz.ch on behalf of Guoneng Zhong
Sent:	Fri 27/05/2005 4:04 PM
To:	bioconductor at stat.math.ethz.ch
Cc:	
Subject:	Re: [BioC] limma reading wrong column for GPR files

The version of limma is 1.9.4 and the R command I executed was:

library(limma)
targets <- readTargets('targets.txt')
f <- function(x) as.numeric(x$Flags > -99)
RG<-read.maimages(targets$FileName,source="genepix",wt.fun=f)

When I typed RG, it shows that the Rf reading for the first row of data 
is the F635 Mean, whereas the Rb reading is B635 Median, and the same 
inconsistency is for the 532 wavelength (Green).  Does anyone see a 
possible problem?  Again. the creator of the GPR file is "GenePix Pro 
3.0.5.56".

Thanks!
G


Marcus Davy wrote:

>You are going to have to supply more information, e.g. version of limma, call to read.maimages, etc.
>
>I downloaded the Genepix 3.0.6 example on the axon website using read.maimages (http://www.axon.com/gn_GPR_Format_History.html) and had no problems correctly populating an RGList with the default columns headers;
>   
>genepix = list(Rf = "F635 Mean", Gf = "F532 Mean", 
>                Rb = "B635 Median", Gb = "B532 Median"),
>
>This was with limma version 1.9.6.
>
>Marcus
>
>  
>
>>>>Guoneng Zhong <guoneng.zhong at yale.edu> 26/05/2005 9:25:16 p.m. >>>
>>>>        
>>>>
>Hi,
>
> I have files generated by Genepix 3.0 and when I use maimages 
>(source="genepix") and checked the RG value (RG being the object created 
>by read.maimages), the red channel foreground reading and the 
>greenchannel foreground reading are swapped (incorrectly), but the 
>background channel are not swapped.  What gives?  Does the latest 
>version of limma know how to read Genepix v. 3 (as opposed to version 
>5/6, which have different column orderings).
>
>Thanks,
>G
>
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