Gordon Smyth wrote: > Dear Yves, > > Thanks for the suggested code changes. Before I make commit changes to > the code, would you mind showing me an example of some headers which > change length? I know that different versions of Imagene produce > different headers, but read.imagene() like read.maimages() is designed > to read a batch of arrays which should in principle have the same > layout, so I would be uncomfortable about users reading in unrelated > arrays. I just want to see in what ways the header can change within one > experiment. You're right, this patch is way too broad; I don't think the headers for the cy3 and cy5 files of a measure can change. > > Note also that if you have two batches of arrays scanned with different > settings, you can read them into two RGList objects and then combine the > objects using cbind. This is the case I met, with slightly different quality settings between the first and subsequent scans. I think it'd be convenient having read.imagene() handle this. Sketch: for (i in 1:narrays) { fullname <- ... + headers <- getImageneHeaders(fullname) + if (headers$Field.Dimensions[...] != printer) error(...) + skip <- headers$Begin.Raw.Data obj<-read.table(...) > > Cheers > Gordon > Regards, yves

I have implemented this in limma 1.2.7. Gordon At 10:43 PM 1/10/2003, Yves Bastide wrote: >Gordon Smyth wrote: >>Dear Yves, >>Thanks for the suggested code changes. Before I make commit changes to >>the code, would you mind showing me an example of some headers which >>change length? I know that different versions of Imagene produce >>different headers, but read.imagene() like read.maimages() is designed to >>read a batch of arrays which should in principle have the same layout, so >>I would be uncomfortable about users reading in unrelated arrays. I just >>want to see in what ways the header can change within one experiment. > >You're right, this patch is way too broad; I don't think the headers for >the cy3 and cy5 files of a measure can change. > >>Note also that if you have two batches of arrays scanned with different >>settings, you can read them into two RGList objects and then combine the >>objects using cbind. > >This is the case I met, with slightly different quality settings between >the first and subsequent scans. I think it'd be convenient having >read.imagene() handle this. > >Sketch: > >for (i in 1:narrays) { > fullname <- ... >+ headers <- getImageneHeaders(fullname) >+ if (headers$Field.Dimensions[...] != printer) error(...) >+ skip <- headers$Begin.Raw.Data > obj<-read.table(...) > >>Cheers >>Gordon > >Regards, > >yves