[BioC] proposal to modify Limma read.maimages generic import

Peter Wilkinson pwilkinson at videotron.ca
Wed Jul 21 18:00:34 CEST 2004

This is a request for Gordon Smyth ...

well, it seems that I have answered my own question "Limma read.maimages 
generic import ".... I think:

The following seems to import the weights just fine, if I am importing from 
a file that contains only the data portion of the quantarray file.

RG.test <- read.maimages("SEKH0406.data", columns=list(Rf="ch2 Intensity",
  Gf="ch1 Intensity" , Rb ="ch2 Background" , Gb ="ch1 Background"), 

The was not immediately evident, since I was using a generic import, 
however the wtIgnore.Filter function is:

 > wtIgnore.Filter
function (qta)
     qta[, "Ignore Filter"]

and that seems to find the right column.

So then I tried the following so that I could include a Garea = "ch1 Area" 
in the column list, because I would like to include area information for 
quality control. This DOES NOT work.

I would like to propose that the function that handles the column input be 
altered so that we can extract any column we wish from the quantarray file 
with the read.maimages function:

If the initialization of the RG object could initialize itself with the 
arbitrary list that is supplied with the columns parameter, then we can 
import whatever data we wish with the generic importer :)

The reason is that I am exploring the use of other information from the 
quantarray output that may help in refining quality weight assignments, but 
I do not want the calculation to be done on import, as I want the data 
available in R. I would have to import every time I wanted to apply a new 
weight function, which would be taxing.

I think that some of the relevant code portions for this modification are:

#       Initialize RG list object
         Y <- matrix(0,nspots,nslides)
         colnames(Y) <- names
         RG <- list(R=Y,G=Y,Rb=Y,Gb=Y)
         if(!is.null(wt.fun)) RG$weights <- Y

change RG assigment to reflect list in columns parameter

#       Now read remainder of files
         for (i in 1:nslides) {
                 if(i > 1) {
                         fullname <- slides[i]
                         if(!is.null(path)) fullname <- 
                         obj <- 
                 RG$R[,i] <- obj[,columns$Rf]
                 RG$G[,i] <- obj[,columns$Gf]
                 RG$Rb[,i] <- obj[,columns$Rb]
                 RG$Gb[,i] <- obj[,columns$Gb]
                 if(!is.null(wt.fun)) RG$weights[,i] <- wt.fun(obj)
                 if(verbose) cat(paste("Read",fullname,"\n"))

modify this portion in the same way.

Would this be sensible? or does there exist another alternative.


At 09:25 AM 7/21/2004, you wrote:

>Hello there,
>I have been pondering over the help files of    'read.maimages' from the 
>limma package when it is used for generic import.
>I have data that I have extracted the data portion of the quantarray 
>files, since alot of the file is just wasting space on the HD. Now I want 
>to import but the data section just looks like a regular square tab 
>delimited file. Is there a parameter (like for specifying which column is 
>R and which is G etc) for specifying the ignore filter column so the 
>ignore filter function can be used to generate the $weights matrix on import?
>I looked at the source code, and I did not see that this was the case, am 
>I correct?
>Peter W.
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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