[BioC] Read.maimages question

[Gordon Smyth]

I think I replied too quickly.

On reading your email again, I think you are intending to specify the 
"Flags" column in the 'annotation' argument to read.maimages(). In that 
case, the second possibility that you mention is true -- the column would 
be read from the first file only and would be stored in a column of RG$genes.

The 'annotation' argument is intended to be used for probe annotation 
columns which do not change from array to array, e.g., chromosome position. 
In GenePix output files, the "Flags" column usually contains spot-specific 
quality flags, and I hadn't intended that 'annotation' be used for a column 
such as that.

Gordon

 > Hi
 >
 > If I read in multiple arrays with the read.maimages() function, and set
 > up "Flags" as one of my annotation columns,

Flags are converted into numeric weights. They would not become an 
"annotation column".

 > does that mean that each of
 > my arrays will be associated with it's individual genepix flags?

Yes, of course, the flags are associated with individual spots.

 > Or are
 > the annotations just read in from one of the arrays, and those
 > annotations then used for all of the arrays in the RGList object?

No, why would you thihk that?  That wouldn't make a lot of sense.

Gordon

 > Thanks
 >
 > Mick