[BioC] limmaGUI and Agilent output files!

[Keith Satterley]

Dear Rafael,

you are mixing up limma and limmaGUI. limmaGUI is the graphical user interface 
to limma. From the list of commands and version number you supply, you are using 
limma with its command line interface.

I maintain limmaGUI, not limma. However I see from the read.maimages code, if an 
annotation option value is not given it assumes the following headings for 
annotations:

agilent = c("Row", "Col", "Start", "Sequence", "SwissProt", "GenBank", 
"Primate", "GenPept", "ProbeUID", "ControlType", "ProbeName", "GeneName", 
"SystematicName", "Description")

The default column names for agilent data columns are set with:

agilent = list(G="gMeanSignal", Gb="gBGMedianSignal", R="rMeanSignal", 
Rb="rBGMedianSignal").

I don't see the need to change Col to Column. (I'm not sure, but it may still 
pick up data from "Column", as "Col" is an unambiguous abbreviation for the 
agilent standard column names).

Also the block information is set with the code:

if(source2=="agilent") {
   if(!is.null(RG$genes$Row) && !is.null(RG$genes$Col)) {
     nr <- length(unique(RG$genes$Row))
     nc <- length(unique(RG$genes$Col))
     if(nspots==nr*nc) RG$printer <- list(ngrid.r=1, ngrid.c=1, nspot.r=nr, 
nspot.c=nc)
  }
}

so your printer layout should be set when data is read in.

What command gives you the memory allocation error. Please supply output from 
sessionInfo() and we may be able to help with the memory allocation problem.

cheers,

Keith

========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
=======================

Gras Peña, Rafael wrote:
>  
> Dear Sir:
>  
> We have been trying to run LimmaGui with our 2 color Agilent chip project (4x44 human, it was scaned with Agilent scan) but it has been imposible. Searching the answer in Internet we have found the following mail:
>  
> "I am having trouble setting up the printer information for an agilent
> data set.  These are the commands I am following:
>> targets <- readTargets()
>> stuff <- read.maimages(targets$FileName,source="agilent")
>> #Setup layout
>> stuff$genes$Block <- 1
>> names(stuff$genes)[2] <- "Column"
>> stuff$printer <- getLayout(stuff$genes)
>> imageplot(log2(stuff$Rb[,1]), stuff$printer, low="white", high="red")
>> Error in imageplot(log2(stuff$Rb[, 1]), stuff$printer, low = "white",  : 
>>         Number of image spots does not agree with layout dimensions
> 
> I added Block information (there is only one block on agilent arrays)
> and changed a column name from "Col" to "Column".  The block is 119x156.
> 
> Any idea what I am doing wrong?
> 
> The printer object gives this:
>> stuff$printer
>> $ngrid.r
>> [1] 1
>>
>> $ngrid.c
>> [1] 1
>>
>> $nspot.r
>> [1] 119
>>
>> $nspot.c
>> [1] 156
>>
>> attr(,"class")
>> [1] "PrintLayout"
>  
> This is our case, but we did not see any answer. We also read this another mail:
> Hi Adrian,
> 
>> I have tried but it doesn't work!
> 
> You need to describe the error in more detail than that
> for us to be able to help you.
> 
> limmaGUI does support Agilent files.  (Just follow the
> instructions in the Swirl example, and replace .spot files
> with your Agilent files.  If you get any errors when you try to
> read the Agilent files into limmaGUI, please report them as
> accurately as possible on this mailing list (including errors
> in message boxes and in the main R console).  Then if you have
> any trouble, we can work out whether the problem is in limma
> (the underlying microarray data analyser) or the GUI (Graphical
> User Interface).  You should also tell us the version number of
> limma and limmaGUI you are using and if possible, send the
> header of one of your Agilent files (i.e. the first few lines,
> before the main table of raw data) and perhaps a few rows of
> the actual raw data.
> 
> Regards,
> James
>  
>  
> But it doesn´t work...
>  
> Our limmaGui version is 2.11.14, and the error message says that "It was not possible to allocate the vector size 176kb". Thank you.
>  
> Regards,
> Rafael
>  
>  
>  
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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