[BioC] problem reading genepix files using both marray andlimma functions

[michael watson (IAH-C)]

>Both read.maimages() and read.GenePix() are designed to read batches of
arrays all corresponding to 
>the same GAL file. You cannot expect to read in data from different GAL
files at one time.

I think this is a VERY important message for everyone who is a beginner
with bioconductor.

All of the data read functions I have come across so far rely on the
files being in the same row-order.  

There is NO cross-referencing of Block/Col/Row or gene names across
files; bioconductor simply assumes that row 1 in file 1 corresponds to
row 1 in file 2, row2 in file 1 to row 2 in file 2 etc etc...

In the vast majority of cases this is fine as most people deal with
batches of files from the same array design which have been produced by
computer, and so the assumption holds.  However, I have come across
cases where this has certainly not been true, and I think new users of
bioconductor are maybe not aware of it.

Mick