 
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
 
 
 
 


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