[BioC] limma and ArrayVision

[alessandro ambrosi]

At 22.11 24/09/03 +1000, Gordon K Smyth wrote:
> > Hi all!
> >
> > I tried to use read.maimages to read ArrayVision files as Gordon
> > suggested. Unfortunately I get the following:
> >
> >  > read.maimages("12371987B.csv", source="arrayvision", sep=",")
> > Error in match.arg(source, c("spot", "spot.close.open", "genepix",
> > "quantarray")) :
> >          ARG should be one of spot, spot.close.open, genepix, quantarray
> >  >
> >



> > I've just updated all the packages so I think this is not the problem.
>
>Yes it is the problem.

:-|   ops!

>   The message that you quote is from limma version
>1.0.8, i.e., the last official BioC release, rather than from limma 1.2.4

sorry, It was under my eyes. The problem was exactly that.
Now read.maimages works perfectly with some file but sometimes fails with
others.
For example

 > read.maimages("2706L.csv", source="arrayvision", sep=",")
Error in "[.data.frame"(obj, , columns$Gb) :
         not all specified columns exist

Probably it's due to some files problem.

Thank you very much.
Best,
Alessandro