[BioC] ArrayVision and limma
smyth at wehi.edu.au
Tue Aug 26 16:50:06 MEST 2003
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:
>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.
>I am attaching an example of a .csv output from ArrayVision if anyone
>would like a crack at it.
>gene expression lab (gele)
>10010 n. torrey pines rd.
>la jolla ca. 92037
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