[BioC] ArrayVision and limma

[Gordon Smyth]

At 12:12 PM 26/08/2003, Isaac Mehl wrote:
>I just received some wonderful help from Jean on reading ArrayVision
>output files into marrayInput. Now i would like to try and analyze with
>limma.  if i understand correctly there is no way to do this unless
>source = "ArrayVision" which doesn't exist.  Read:
>https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-August/002182.html
>which leads me to believe that the only way to accomplish this is for
>Gordon to write a separate function.  Is this the only way to read in
>data?  Won't this be a pain with many, many different software packages
>making spot calls??  Isn't it possible to simply specify which column
>contains the needed information (RF, Gf, Rb, etc) in a matrix??

I don't see the problem. If you've read in the data using marrayInput and 
then normalized using marrayNorm, you can use any of the linear model 
functions in limma to analyse your data, as explained in the section called 
"Using limma with the marray Packages" in the LIMMA User's Guide. The 
easiest function to use would be 'lmFit', in the development version of 
limma, because it accepts 'marrayNorm' objects directly.

If for some reason you want to read in your data using limma instead of 
marrayNorm, you could do so by using the 'columns' argument of 
'read.maimages' to specify which columns of your data files correspond to 
Rf, Gf, Rb and Gb. This option has always been available in limma, although 
the development version of limma will do a better job of handling column 
names containing spaces, like the names in your file. As the help document 
for 'read.maimages' says,

    "At present, the image analysis programs SPOT, GenePix, QuantArray
    and Imagene are supported. Other image analysis programs can
    potentially be accommodated though a user-specified 'columns' argument."

The reason that Imagene data required special intervention from me was (i) 
because Imagene is almost unique in that it writes the red and green 
channel information to separate files and (ii) because neither limma nor 
marrayNorm supported imagene explicitly.

Gordon

>I am attaching an example of a .csv output from ArrayVision if anyone
>would like a crack at it.
>--
>-isaac mehl
>gene expression lab (gele)
>salk institute
>10010 n. torrey pines rd.
>la jolla ca. 92037
>http://genex.salk.edu