[BioC] Read.maimages question
Gordon Smyth
smyth at wehi.edu.au
Thu Sep 2 06:40:29 CEST 2004
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
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