Hi If I read in multiple arrays with the read.maimages() function, and set up "Flags" as one of my annotation columns, does that mean that each of my arrays will be associated with it's individual genepix flags? 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? Thanks Mick

> 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

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

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@wehi.edu.au] Sent: 02 September 2004 05:40 To: michael watson (IAH-C) Cc: bioconductor@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