[BioC] Read.maimages question

[michael watson (IAH-C)]

Thank you, that is what I expected :-)

What I am trying to do is to link the flag information to the final
results in limma as produced by topTable() (for example).  If I simply
read my data in, normalise it, fit a model and the run off with the
results, I might miss the fact that all the replicate measurements of
one of my differentially expressed genes had flags of -50.

So what I am trying to do is summarise the flags for each spot over all
replicate arrays, and then append that summary to the results of
topTable().  I realise this isn't as subtle as creating weights for each
spot based on their flags, but sometimes I prefer to do the former.

Cheers
Mick

-----Original Message-----
From: Gordon Smyth [mailto:smyth at wehi.edu.au] 
Sent: 02 September 2004 05:40
To: michael watson (IAH-C)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Read.maimages question


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