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

[Gordon Smyth]

At 06:11 PM 18/08/2004, michael watson (IAH-C) wrote:
> >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.

True enough. ?read.maimages has a section called "Warnings:" which cautions 
on exactly this point.

Gordon

>Mick